--- title: "Get structure by ENTRY ID." method: GET path: "/rest/v1/core/entry/{entry_id}" tags: ["Entry Service"] --- # Get structure by ENTRY ID. `GET /rest/v1/core/entry/{entry_id}` ## Request - Base URL: `https://data.rcsb.org` - URL: `https://data.rcsb.org/rest/v1/core/entry/{entry_id}` - Auth: none declared - TypeScript: (a function with typed inputs; its response is checked against the schema) ## Path parameters - `entry_id` string, required ## Response `200` OK - CoreEntry - `audit_author` AuditAuthor[] - `identifier_ORCID` string: The Open Researcher and Contributor ID (ORCID). - `name` string: The name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). - `pdbx_ordinal` integer, required: This data item defines the order of the author's name in the list of audit authors. - `cell` Cell - `Z_PDB` integer: The number of the polymeric chains in a unit cell. In the case of heteropolymers, Z is the number of occurrences of the most populous chain. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. - `angle_alpha` number, double: Unit-cell angle alpha of the reported structure in degrees. - `angle_beta` number, double: Unit-cell angle beta of the reported structure in degrees. - `angle_gamma` number, double: Unit-cell angle gamma of the reported structure in degrees. - `formula_units_Z` integer: The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum. - `length_a` number, double: Unit-cell length a corresponding to the structure reported in angstroms. - `length_b` number, double: Unit-cell length b corresponding to the structure reported in angstroms. - `length_c` number, double: Unit-cell length c corresponding to the structure reported in angstroms. - `pdbx_unique_axis` string: To further identify unique axis if necessary. E.g., P 21 with an unique C axis will have 'C' in this field. - `volume` number, double: Cell volume V in angstroms cubed. V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~ + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^ a = _cell.length_a b = _cell.length_b c = _cell.length_c alpha = _cell.angle_alpha beta = _cell.angle_beta gamma = _cell.angle_gamma - `citation` Citation[] - `book_id_ISBN` string: The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters. - `book_publisher` string: The name of the publisher of the citation; relevant for books or book chapters. - `book_publisher_city` string: The location of the publisher of the citation; relevant for books or book chapters. - `book_title` string: The title of the book in which the citation appeared; relevant for books or book chapters. - `coordinate_linkage` 'n' | 'no' | 'y' | 'yes': _citation.coordinate_linkage states whether this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to the creation of the data block, the value of this data item would be 'no'. - `country` string: The country/region of publication; relevant for books and book chapters. - `id` string, required: The value of _citation.id must uniquely identify a record in the CITATION list. The _citation.id 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. - `journal_abbrev` string: Abbreviated name of the cited journal as given in the Chemical Abstracts Service Source Index. - `journal_full` string: Full name of the cited journal; relevant for journal articles. - `journal_id_ASTM` string: The American Society for Testing and Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. - `journal_id_CSD` string: The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Protein Data Bank (PDB). - `journal_id_ISSN` string: The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. - `journal_issue` string: Issue number of the journal cited; relevant for journal articles. - `journal_volume` string: Volume number of the journal cited; relevant for journal articles. - `language` string: Language in which the cited article is written. - `page_first` string: The first page of the citation; relevant for journal articles, books and book chapters. - `page_last` string: The last page of the citation; relevant for journal articles, books and book chapters. - `pdbx_database_id_DOI` string: Document Object Identifier used by doi.org to uniquely specify bibliographic entry. - `pdbx_database_id_PubMed` integer: Ascession number used by PubMed to categorize a specific bibliographic entry. - `rcsb_authors` string[]: Names of the authors of the citation; relevant for journal articles, books and book chapters. Names are separated by vertical bars. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). - `rcsb_is_primary` 'N' | 'Y': Flag to indicate a primary citation. - `rcsb_journal_abbrev` string: Normalized journal abbreviation. - `title` string: The title of the citation; relevant for journal articles, books and book chapters. - `unpublished_flag` 'N' | 'Y': Flag to indicate that this citation will not be published. - `year` integer: The year of the citation; relevant for journal articles, books and book chapters. - `database_2` Database2[] - `database_code` string, required: The code assigned by the database identified in _database_2.database_id. - `database_id` 'AlphaFoldDB' | 'BMRB' | 'EBI' | 'EMDB' | 'MODBASE' | 'ModelArchive' | 'NDB' | 'PDB' | 'PDB-Dev' | 'PDBE' | 'PDB_ACC' | 'RCSB' | 'SWISS-MODEL_REPOSITORY' | 'WWPDB', required: An abbreviation that identifies the database. - `pdbx_DOI` string: Document Object Identifier (DOI) for this entry registered with http://crossref.org. - `pdbx_database_accession` string: Extended accession code issued for for _database_2.database_code assigned by the database identified in _database_2.database_id. - `diffrn` Diffrn[] - `ambient_pressure` number, double: The mean hydrostatic pressure in kilopascals at which the intensities were measured. - `ambient_temp` number, double: The mean temperature in kelvins at which the intensities were measured. - `ambient_temp_details` string: A description of special aspects of temperature control during data collection. - `crystal_id` string: This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. - `crystal_support` string: The physical device used to support the crystal during data collection. - `details` string: Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on. - `id` string, required: This data item uniquely identifies a set of diffraction data. - `pdbx_serial_crystal_experiment` 'N' | 'Y': Y/N if using serial crystallography experiment in which multiple crystals contribute to each diffraction frame in the experiment. - `diffrn_detector` DiffrnDetector[] - `details` string: A description of special aspects of the radiation detector. - `detector` string: The general class of the radiation detector. - `diffrn_id` string, required: This data item is a pointer to _diffrn.id in the DIFFRN category. - `pdbx_collection_date` string, date-time: The date of data collection. - `pdbx_frequency` number, double: The operating frequency of the detector (Hz) used in data collection. - `type` string: The make, model or name of the detector device used. - `diffrn_radiation` DiffrnRadiation[] - `collimation` string: The collimation or focusing applied to the radiation. - `diffrn_id` string, required: This data item is a pointer to _diffrn.id in the DIFFRN category. - `monochromator` string: The method used to obtain monochromatic radiation. If a mono- chromator crystal is used, the material and the indices of the Bragg reflection are specified. - `pdbx_diffrn_protocol` string: SINGLE WAVELENGTH, LAUE, or MAD. - `pdbx_monochromatic_or_laue_m_l` 'L' | 'M': Monochromatic or Laue. - `pdbx_scattering_type` 'electron' | 'neutron' | 'x-ray': The radiation scattering type for this diffraction data set. - `pdbx_wavelength` string: Wavelength of radiation. - `pdbx_wavelength_list` string: Comma separated list of wavelengths or wavelength range. - `type` string: The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation. - `wavelength_id` string: This data item is a pointer to _diffrn_radiation_wavelength.id in the DIFFRN_RADIATION_WAVELENGTH category. - `diffrn_source` DiffrnSource[] - `details` string: A description of special aspects of the radiation source used. - `diffrn_id` string, required: This data item is a pointer to _diffrn.id in the DIFFRN category. - `pdbx_synchrotron_beamline` string: Synchrotron beamline. - `pdbx_synchrotron_site` string: Synchrotron site. - `pdbx_wavelength` string: Wavelength of radiation. - `pdbx_wavelength_list` string: Comma separated list of wavelengths or wavelength range. - `source` string: The general class of the radiation source. - `type` string: The make, model or name of the source of radiation. - `em_2d_crystal_entity` Em2dCrystalEntity[] - `angle_gamma` number, double: Unit-cell angle gamma in degrees. - `c_sampling_length` number, double: Length used to sample the reciprocal lattice lines in the c-direction. - `id` string, required: PRIMARY KEY - `image_processing_id` string, required: pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. - `length_a` number, double: Unit-cell length a in angstroms. - `length_b` number, double: Unit-cell length b in angstroms. - `length_c` number, double: Thickness of 2D crystal - `space_group_name_H_M` 'C 1 2' | 'C 2 2 2' | 'P 1' | 'P 1 2' | 'P 1 21' | 'P 2' | 'P 2 2 2' | 'P 2 2 21' | 'P 2 21 21' | 'P 3' | 'P 3 1 2' | 'P 3 2 1' | 'P 4' | 'P 4 2 2' | 'P 4 21 2' | 'P 6' | 'P 6 2 2': There are 17 plane groups classified as oblique, rectangular, square, and hexagonal. To describe the symmetry of 2D crystals of biological molecules, plane groups are expanded to equivalent noncentrosymmetric space groups. The 2D crystal plane corresponds to the 'ab' plane of the space group. Enumerated space group descriptions include the plane group number in parentheses, the H-M plane group symbol, and the plane group class. - `em_3d_crystal_entity` Em3dCrystalEntity[] - `angle_alpha` number, double: Unit-cell angle alpha in degrees. - `angle_beta` number, double: Unit-cell angle beta in degrees. - `angle_gamma` number, double: Unit-cell angle gamma in degrees. - `id` string, required: PRIMARY KEY - `image_processing_id` string, required: pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. - `length_a` number, double: Unit-cell length a in angstroms. - `length_b` number, double: Unit-cell length b in angstroms. - `length_c` number, double: Unit-cell length c in angstroms. - `space_group_name` string: Space group name. - `space_group_num` integer: Space group number. - `em_3d_fitting` Em3dFitting[] - `details` string: Any additional details regarding fitting of atomic coordinates into the 3DEM volume, including data and considerations from other methods used in computation of the model. - `id` string, required: The value of _em_3d_fitting.id must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed map volume. - `method` string: The method used to fit atomic coordinates into the 3dem reconstructed map. - `overall_b_value` number, double: The overall B (temperature factor) value for the 3d-em volume. - `ref_protocol` 'AB INITIO MODEL' | 'BACKBONE TRACE' | 'FLEXIBLE FIT' | 'OTHER' | 'RIGID BODY FIT': The refinement protocol used. - `ref_space` 'REAL' | 'RECIPROCAL': A flag to indicate whether fitting was carried out in real or reciprocal refinement space. - `target_criteria` string: The measure used to assess quality of fit of the atomic coordinates in the 3DEM map volume. - `em_3d_fitting_list` Em3dFittingList[] - `3d_fitting_id` string, required: The value of _em_3d_fitting_list.3d_fitting_id is a pointer to _em_3d_fitting.id in the 3d_fitting category - `details` string: Details about the model used in fitting. - `id` string, required: PRIMARY KEY - `pdb_chain_id` string: The ID of the biopolymer chain used for fitting, e.g., A. Please note that only one chain can be specified per instance. If all chains of a particular structure have been used for fitting, this field can be left blank. - `pdb_chain_residue_range` string: Residue range for the identified chain. - `pdb_entry_id` string: The PDB code for the entry used in fitting. - `em_3d_reconstruction` Em3dReconstruction[] - `actual_pixel_size` number, double: The actual pixel size of the projection set of images in Angstroms. - `algorithm` string: The reconstruction algorithm/technique used to generate the map. - `details` string: Any additional details used in the 3d reconstruction. - `id` string, required: PRIMARY KEY - `image_processing_id` string, required: Foreign key to the EM_IMAGE_PROCESSING category - `magnification_calibration` string: The magnification calibration method for the 3d reconstruction. - `method` string: The algorithm method used for the 3d-reconstruction. - `nominal_pixel_size` number, double: The nominal pixel size of the projection set of images in Angstroms. - `num_class_averages` integer: The number of classes used in the final 3d reconstruction - `num_particles` integer: The number of 2D projections or 3D subtomograms used in the 3d reconstruction - `refinement_type` 'HALF-MAPS REFINED AGAINST SAME DATA' | 'HALF-MAPS REFINED INDEPENDENTLY' | 'HALF-MAPS REFINED INDEPENDENTLY WITH FREQUENCY RANGE OMITTED' | 'HALF-MAPS REFINED WITH FREQUENCY RANGE OMITTED' | 'OTHER': Indicates details on how the half-map used for resolution determination (usually by FSC) have been generated. - `resolution` number, double: The final resolution (in angstroms) of the 3D reconstruction. - `resolution_method` string: The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. - `symmetry_type` '2D CRYSTAL' | '3D CRYSTAL' | 'HELICAL' | 'POINT': The type of symmetry applied to the reconstruction - `em_ctf_correction` EmCtfCorrection[] - `details` string: Any additional details about CTF correction - `em_image_processing_id` string: Foreign key to the EM_IMAGE_PROCESSING category - `id` string, required: PRIMARY KEY - `type` string: Type of CTF correction applied - `em_diffraction` EmDiffraction[] - `camera_length` number, double: The camera length (in millimeters). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. - `id` string, required: PRIMARY KEY - `imaging_id` string: Foreign key to the EM_IMAGING category - `tilt_angle_list` string: Comma-separated list of tilt angles (in degrees) used in the electron diffraction experiment. - `em_diffraction_shell` EmDiffractionShell[] - `em_diffraction_stats_id` string: Pointer to EM CRYSTALLOGRAPHY STATS - `fourier_space_coverage` number, double: Completeness of the structure factor data within this resolution shell, in percent - `high_resolution` number, double: High resolution limit for this shell (angstroms) - `id` string, required: PRIMARY KEY - `low_resolution` number, double: Low resolution limit for this shell (angstroms) - `multiplicity` number, double: Multiplicity (average number of measurements) for the structure factors in this resolution shell - `num_structure_factors` integer: Number of measured structure factors in this resolution shell - `phase_residual` number, double: Phase residual for this resolution shell, in degrees - `em_diffraction_stats` EmDiffractionStats[] - `details` string: Any addition details about the structure factor measurements - `fourier_space_coverage` number, double: Completeness of the structure factor data within the defined space group at the reported resolution (percent). - `high_resolution` number, double: High resolution limit of the structure factor data, in angstroms - `id` string, required: PRIMARY KEY - `image_processing_id` string: Pointer to _em_image_processing.id - `num_intensities_measured` integer: Total number of diffraction intensities measured (before averaging) - `num_structure_factors` integer: Number of structure factors obtained (merged amplitudes + phases) - `overall_phase_error` number, double: Overall phase error in degrees - `overall_phase_residual` number, double: Overall phase residual in degrees - `phase_error_rejection_criteria` string: Criteria used to reject phases - `r_merge` number, double: Rmerge value (percent) - `r_sym` number, double: Rsym value (percent) - `em_embedding` EmEmbedding[] - `details` string: Staining procedure used in the specimen preparation. - `id` string, required: PRIMARY KEY - `material` string: The embedding material. - `specimen_id` string: Foreign key relationship to the EM SPECIMEN category - `em_entity_assembly` EmEntityAssembly[] - `details` string: Additional details about the sample or sample subcomponent. - `entity_id_list` string[]: macromolecules associated with this component, if defined as comma separated list of entity ids (integers). - `id` string, required: PRIMARY KEY - `name` string: The name of the sample or sample subcomponent. - `oligomeric_details` string: oligomeric details - `parent_id` integer: The parent of this assembly. This data item is an internal category pointer to _em_entity_assembly.id. By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero). - `source` 'MULTIPLE SOURCES' | 'NATURAL' | 'RECOMBINANT' | 'SYNTHETIC': The type of source (e.g., natural source) for the component (sample or sample subcomponent) - `synonym` string: Alternative name of the component. - `type` string: The general type of the sample or sample subcomponent. - `em_experiment` EmExperiment - `aggregation_state` '2D ARRAY' | '3D ARRAY' | 'CELL' | 'FILAMENT' | 'HELICAL ARRAY' | 'PARTICLE' | 'TISSUE': The aggregation/assembly state of the imaged specimen. - `entity_assembly_id` string: Foreign key to the EM_ENTITY_ASSEMBLY category - `id` string: PRIMARY KEY - `reconstruction_method` 'CRYSTALLOGRAPHY' | 'HELICAL' | 'SINGLE PARTICLE' | 'SUBTOMOGRAM AVERAGING' | 'TOMOGRAPHY': The reconstruction method used in the EM experiment. - `em_helical_entity` EmHelicalEntity[] - `angular_rotation_per_subunit` number, double: The angular rotation per helical subunit in degrees. Negative values indicate left-handed helices; positive values indicate right handed helices. - `axial_rise_per_subunit` number, double: The axial rise per subunit in the helical assembly. - `axial_symmetry` string: Symmetry of the helical axis, either cyclic (Cn) or dihedral (Dn), where n>=1. - `details` string: Any other details regarding the helical assembly - `id` string, required: PRIMARY KEY - `image_processing_id` string, required: This data item is a pointer to _em_image_processing.id. - `em_image_recording` EmImageRecording[] - `average_exposure_time` number, double: The average exposure time for each image. - `avg_electron_dose_per_image` number, double: The electron dose received by the specimen per image (electrons per square angstrom). - `details` string: Any additional details about image recording. - `detector_mode` 'COUNTING' | 'INTEGRATING' | 'OTHER' | 'SUPER-RESOLUTION': The detector mode used during image recording. - `film_or_detector_model` string: The detector type used for recording images. Usually film , CCD camera or direct electron detector. - `id` string, required: PRIMARY KEY - `imaging_id` string, required: This data item the id of the microscopy settings used in the imaging. - `num_diffraction_images` integer: The number of diffraction images collected. - `num_grids_imaged` integer: Number of grids in the microscopy session - `num_real_images` integer: The number of micrograph images collected. - `em_imaging` EmImaging[] - `accelerating_voltage` integer: A value of accelerating voltage (in kV) used for imaging. - `alignment_procedure` 'BASIC' | 'COMA FREE' | 'NONE' | 'OTHER' | 'ZEMLIN TABLEAU': The type of procedure used to align the microscope electron beam. - `astigmatism` string: astigmatism - `c2_aperture_diameter` number, double: The open diameter of the c2 condenser lens, in microns. - `calibrated_defocus_max` number, double: The maximum calibrated defocus value of the objective lens (in nanometres) used to obtain the recorded images. Negative values refer to overfocus. - `calibrated_defocus_min` number, double: The minimum calibrated defocus value of the objective lens (in nanometres) used to obtain the recorded images. Negative values refer to overfocus. - `calibrated_magnification` integer: The magnification value obtained for a known standard just prior to, during or just after the imaging experiment. - `cryogen` 'HELIUM' | 'NITROGEN': Cryogen type used to maintain the specimen stage temperature during imaging in the microscope. - `date` string, date-time: Date (YYYY-MM-DD) of imaging experiment or the date at which a series of experiments began. - `details` string: Any additional imaging details. - `detector_distance` number, double: The camera length (in millimeters). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. - `electron_beam_tilt_params` string: electron beam tilt params - `electron_source` string: The source of electrons. The electron gun. - `id` string, required: PRIMARY KEY - `illumination_mode` 'FLOOD BEAM' | 'OTHER' | 'SPOT SCAN': The mode of illumination. - `microscope_model` 'FEI MORGAGNI' | 'FEI POLARA 300' | 'FEI TALOS ARCTICA' | 'FEI TECNAI 10' | 'FEI TECNAI 12' | 'FEI TECNAI 20' | 'FEI TECNAI ARCTICA' | 'FEI TECNAI F20' | 'FEI TECNAI F30' | 'FEI TECNAI SPHERA' | 'FEI TECNAI SPIRIT' | 'FEI TITAN' | 'FEI TITAN KRIOS' | 'FEI/PHILIPS CM10' | 'FEI/PHILIPS CM12' | 'FEI/PHILIPS CM120T' | 'FEI/PHILIPS CM200FEG' | 'FEI/PHILIPS CM200FEG/SOPHIE' | 'FEI/PHILIPS CM200FEG/ST' | 'FEI/PHILIPS CM200FEG/UT' | 'FEI/PHILIPS CM200T' | 'FEI/PHILIPS CM300FEG/HE' | 'FEI/PHILIPS CM300FEG/ST' | 'FEI/PHILIPS CM300FEG/T' | 'FEI/PHILIPS EM400' | 'FEI/PHILIPS EM420' | 'HITACHI EF2000' | 'HITACHI EF3000' | 'HITACHI H-9500SD' | 'HITACHI H3000 UHVEM' | 'HITACHI H7600' | 'HITACHI HF2000' | 'HITACHI HF3000' | 'JEOL 1000EES' | 'JEOL 100B' | 'JEOL 100CX' | 'JEOL 1010' | 'JEOL 1200' | 'JEOL 1200EX' | 'JEOL 1200EXII' | 'JEOL 1230' | 'JEOL 1400' | 'JEOL 1400/HR + YPS FEG' | 'JEOL 2000EX' | 'JEOL 2000EXII' | 'JEOL 2010' | 'JEOL 2010F' | 'JEOL 2010HC' | 'JEOL 2010HT' | 'JEOL 2010UHR' | 'JEOL 2011' | 'JEOL 2100' | 'JEOL 2100F' | 'JEOL 2200FS' | 'JEOL 2200FSC' | 'JEOL 3000SFF' | 'JEOL 3100FEF' | 'JEOL 3100FFC' | 'JEOL 3200FS' | 'JEOL 3200FSC' | 'JEOL 4000' | 'JEOL 4000EX' | 'JEOL CRYO ARM 200' | 'JEOL CRYO ARM 300' | 'JEOL JEM-F200' | 'JEOL KYOTO-3000SFF' | 'SHUIMU TOTEM 120S' | 'SHUIMU TOTEM 200S' | 'SHUIMU TOTEM 300S' | 'SIEMENS SULEIKA' | 'TFS GLACIOS' | 'TFS KRIOS' | 'TFS TALOS' | 'TFS TALOS F200C' | 'TFS TALOS L120C' | 'TFS TITAN THEMIS' | 'TFS TUNDRA' | 'ZEISS LEO912' | 'ZEISS LIBRA120PLUS': The name of the model of microscope. - `mode` '4D-STEM' | 'BRIGHT FIELD' | 'DARK FIELD' | 'DIFFRACTION' | 'OTHER': The mode of imaging. - `nominal_cs` number, double: The spherical aberration coefficient (Cs) in millimeters, of the objective lens. - `nominal_defocus_max` number, double: The maximum defocus value of the objective lens (in nanometres) used to obtain the recorded images. Negative values refer to overfocus. - `nominal_defocus_min` number, double: The minimum defocus value of the objective lens (in nanometres) used to obtain the recorded images. Negative values refer to overfocus. - `nominal_magnification` integer: The magnification indicated by the microscope readout. - `recording_temperature_maximum` number, double: The specimen temperature maximum (kelvin) for the duration of imaging. - `recording_temperature_minimum` number, double: The specimen temperature minimum (kelvin) for the duration of imaging. - `residual_tilt` number, double: Residual tilt of the electron beam (in miliradians) - `specimen_holder_model` 'FEI TITAN KRIOS AUTOGRID HOLDER' | 'FISCHIONE 2550' | 'FISCHIONE INSTRUMENTS DUAL AXIS TOMOGRAPHY HOLDER' | 'GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER' | 'GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER' | 'GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER' | 'GATAN 915 DOUBLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER' | 'GATAN CHDT 3504 DOUBLE TILT HIGH RESOLUTION NITROGEN COOLING HOLDER' | 'GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER' | 'GATAN CT3500TR SINGLE TILT ROTATION LIQUID NITROGEN CRYO TRANSFER HOLDER' | 'GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER' | 'GATAN HC 3500 SINGLE TILT HEATING/NITROGEN COOLING HOLDER' | 'GATAN HCHDT 3010 DOUBLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER' | 'GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER' | 'GATAN HELIUM' | 'GATAN LIQUID NITROGEN' | 'GATAN UHRST 3500 SINGLE TILT ULTRA HIGH RESOLUTION NITROGEN COOLING HOLDER' | 'GATAN ULTDT ULTRA LOW TEMPERATURE DOUBLE TILT HELIUM COOLING HOLDER' | 'GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER' | 'HOME BUILD' | 'JEOL' | 'JEOL 3200FSC CRYOHOLDER' | 'JEOL CRYOSPECPORTER' | 'OTHER' | 'PHILIPS ROTATION HOLDER' | 'SIDE ENTRY, EUCENTRIC': The name of the model of specimen holder used during imaging. - `specimen_holder_type` string: The type of specimen holder used during imaging. - `specimen_id` string: Foreign key to the EM_SPECIMEN category - `temperature` number, double: The mean specimen stage temperature (in kelvin) during imaging in the microscope. - `tilt_angle_max` number, double: The maximum angle at which the specimen was tilted to obtain recorded images. - `tilt_angle_min` number, double: The minimum angle at which the specimen was tilted to obtain recorded images. - `em_particle_selection` EmParticleSelection[] - `details` string: Additional detail such as description of filters used, if selection was manual or automated, and/or template details. - `id` string, required: PRIMARY KEY - `image_processing_id` string, required: The value of _em_particle_selection.image_processing_id points to the EM_IMAGE_PROCESSING category. - `num_particles_selected` integer: The number of particles selected from the projection set of images. - `em_single_particle_entity` EmSingleParticleEntity[] - `id` integer, required: PRIMARY KEY - `image_processing_id` string, required: pointer to _em_image_processing.id. - `point_symmetry` string: Point symmetry symbol, either Cn, Dn, T, O, or I - `em_software` EmSoftware[] - `category` 'CLASSIFICATION' | 'CRYSTALLOGRAPHY MERGING' | 'CTF CORRECTION' | 'DIFFRACTION INDEXING' | 'EWALD SPHERE CORRECTION' | 'FINAL EULER ASSIGNMENT' | 'IMAGE ACQUISITION' | 'INITIAL EULER ASSIGNMENT' | 'LATTICE DISTORTION CORRECTION' | 'LAYERLINE INDEXING' | 'MASKING' | 'MODEL FITTING' | 'MODEL REFINEMENT' | 'MOLECULAR REPLACEMENT' | 'OTHER' | 'PARTICLE SELECTION' | 'RECONSTRUCTION' | 'SERIES ALIGNMENT' | 'SYMMETRY DETERMINATION' | 'VOLUME SELECTION': The purpose of the software. - `details` string: Details about the software used. - `fitting_id` string: pointer to _em_3d_fitting.id in the EM_3D_FITTING category. - `id` string, required: PRIMARY KEY - `image_processing_id` string: pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. - `imaging_id` string: pointer to _em_imaging.id in the EM_IMAGING category. - `name` string: The name of the software package used, e.g., RELION. Depositors are strongly encouraged to provide a value in this field. - `version` string: The version of the software. - `em_specimen` EmSpecimen[] - `concentration` number, double: The concentration (in milligrams per milliliter, mg/ml) of the complex in the sample. - `details` string: A description of any additional details of the specimen preparation. - `embedding_applied` 'NO' | 'YES': 'YES' indicates that the specimen has been embedded. - `experiment_id` string, required: Pointer to _em_experiment.id. - `id` string, required: PRIMARY KEY - `shadowing_applied` 'NO' | 'YES': 'YES' indicates that the specimen has been shadowed. - `staining_applied` 'NO' | 'YES': 'YES' indicates that the specimen has been stained. - `vitrification_applied` 'NO' | 'YES': 'YES' indicates that the specimen was vitrified by cryopreservation. - `em_staining` EmStaining[] - `details` string: Staining procedure used in the specimen preparation. - `id` string, required: PRIMARY KEY - `material` string: The staining material. - `specimen_id` string: Foreign key relationship to the EM SPECIMEN category - `type` 'NEGATIVE' | 'NONE' | 'POSITIVE': type of staining - `em_vitrification` EmVitrification[] - `chamber_temperature` number, double: The temperature (in kelvin) of the sample just prior to vitrification. - `cryogen_name` 'ETHANE' | 'ETHANE-PROPANE' | 'FREON 12' | 'FREON 22' | 'HELIUM' | 'METHANE' | 'NITROGEN' | 'OTHER' | 'PROPANE': This is the name of the cryogen. - `details` string: Any additional details relating to vitrification. - `humidity` number, double: Relative humidity (%) of air surrounding the specimen just prior to vitrification. - `id` string, required: PRIMARY KEY - `instrument` 'CHAMELEON' | 'CRYOGENIUM' | 'CRYOSOL VITROJET' | 'CRYOWRITER' | 'EMS-002 RAPID IMMERSION FREEZER' | 'FEI VITROBOT MARK I' | 'FEI VITROBOT MARK II' | 'FEI VITROBOT MARK III' | 'FEI VITROBOT MARK IV' | 'GATAN CRYOPLUNGE 3' | 'HOMEMADE PLUNGER' | 'LEICA EM CPC' | 'LEICA EM GP' | 'LEICA EM GP2' | 'LEICA KF80' | 'LEICA PLUNGER' | 'REICHERT-JUNG PLUNGER' | 'SPOTITON' | 'SPT LABTECH CHAMELEON' | 'ZEISS PLUNGE FREEZER CRYOBOX': The type of instrument used in the vitrification process. - `method` string: The procedure for vitrification. - `specimen_id` string, required: This data item is a pointer to _em_specimen.id - `temp` number, double: The vitrification temperature (in kelvin), e.g., temperature of the plunge instrument cryogen bath. - `time_resolved_state` string: The length of time after an event effecting the sample that vitrification was induced and a description of the event. - `entry` Entry - `id` string, required: The value of _entry.id identifies the data block. Note that this item need not be a number; it can be any unique identifier. - `ma_collection_id` string: An identifier for the model collection associated with the entry. - `exptl` Exptl[] - `crystals_number` integer: The total number of crystals used in the measurement of intensities. - `details` string: Any special information about the experimental work prior to the intensity measurement. See also _exptl_crystal.preparation. - `method` 'ELECTRON CRYSTALLOGRAPHY' | 'ELECTRON MICROSCOPY' | 'EPR' | 'FIBER DIFFRACTION' | 'FLUORESCENCE TRANSFER' | 'INFRARED SPECTROSCOPY' | 'NEUTRON DIFFRACTION' | 'POWDER DIFFRACTION' | 'SOLID-STATE NMR' | 'SOLUTION NMR' | 'SOLUTION SCATTERING' | 'THEORETICAL MODEL' | 'X-RAY DIFFRACTION', required: The method used in the experiment. - `method_details` string: A description of special aspects of the experimental method. - `exptl_crystal` ExptlCrystal[] - `colour` string: The colour of the crystal. - `density_Matthews` number, double: The density of the crystal, expressed as the ratio of the volume of the asymmetric unit to the molecular mass of a monomer of the structure, in units of angstroms^3^ per dalton. Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497. - `density_meas` number, double: Density values measured using standard chemical and physical methods. The units are megagrams per cubic metre (grams per cubic centimetre). - `density_percent_sol` number, double: Density value P calculated from the crystal cell and contents, expressed as per cent solvent. P = 1 - (1.23 N MMass) / V N = the number of molecules in the unit cell MMass = the molecular mass of each molecule (gm/mole) V = the volume of the unit cell (A^3^) 1.23 = a conversion factor evaluated as: (0.74 cm^3^/g) (10^24^ A^3^/cm^3^) -------------------------------------- (6.02*10^23^) molecules/mole where 0.74 is an assumed value for the partial specific volume of the molecule - `description` string: A description of the quality and habit of the crystal. The crystal dimensions should not normally be reported here; use instead the specific items in the EXPTL_CRYSTAL category relating to size for the gross dimensions of the crystal and data items in the EXPTL_CRYSTAL_FACE category to describe the relationship between individual faces. - `id` string, required: The value of _exptl_crystal.id must uniquely identify a record in the EXPTL_CRYSTAL list. Note that this item need not be a number; it can be any unique identifier. - `pdbx_mosaicity` number, double: Isotropic approximation of the distribution of mis-orientation angles specified in degrees of all the mosaic domain blocks in the crystal, represented as a standard deviation. Here, a mosaic block is a set of contiguous unit cells assumed to be perfectly aligned. Lower mosaicity indicates better ordered crystals. See for example: Nave, C. (1998). Acta Cryst. D54, 848-853. Note that many software packages estimate the mosaic rotation distribution differently and may combine several physical properties of the experiment into a single mosaic term. This term will help fit the modeled spots to the observed spots without necessarily being directly related to the physics of the crystal itself. - `pdbx_mosaicity_esd` number, double: The uncertainty in the mosaicity estimate for the crystal. - `preparation` string: Details of crystal growth and preparation of the crystal (e.g. mounting) prior to the intensity measurements. - `exptl_crystal_grow` ExptlCrystalGrow[] - `crystal_id` string, required: This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. - `details` string: A description of special aspects of the crystal growth. - `method` string: The method used to grow the crystals. - `pH` number, double: The pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in _exptl_crystal_grow.details. - `pdbx_details` string: Text description of crystal growth procedure. - `pdbx_pH_range` string: The range of pH values at which the crystal was grown. Used when a point estimate of pH is not appropriate. - `temp` number, double: The temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in _exptl_crystal_grow.details. - `temp_details` string: A description of special aspects of temperature control during crystal growth. - `ihm_entry_collection_mapping` IhmEntryCollectionMapping[] - `collection_id` string, required: Identifier for the entry collection. This data item is a pointer to _ihm_entry_collection.id in the IHM_ENTRY_COLLECTION category. - `ihm_external_reference_info` IhmExternalReferenceInfo[] - `associated_url` string: The Uniform Resource Locator (URL) corresponding to the external reference (DOI). This URL should link to the corresponding downloadable file or archive and is provided to enable automated software to download the referenced file or archive. - `reference` string: The external reference or the Digital Object Identifier (DOI). This field is not relevant for local files. - `reference_provider` string: The name of the reference provider. - `ma_data` MaData[] - `content_type` 'coevolution MSA' | 'input structure' | 'model coordinates' | 'other' | 'polymeric template library' | 'reference database' | 'spatial restraints' | 'target' | 'target-template alignment' | 'template structure': The type of data held in the dataset. - `content_type_other_details` string: Details for other content types. - `id` integer, required: A unique identifier for the data. - `name` string: An author-given name for the content held in the dataset. - `pdbx_SG_project` PdbxSGProject[] - `full_name_of_center` 'Accelerated Technologies Center for Gene to 3D Structure' | 'Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions' | 'Atoms-to-Animals: The Immune Function Network' | 'Bacterial targets at IGS-CNRS, France' | 'Berkeley Structural Genomics Center' | 'Center for Eukaryotic Structural Genomics' | 'Center for High-Throughput Structural Biology' | 'Center for Membrane Proteins of Infectious Diseases' | 'Center for Structural Biology of Infectious Diseases' | 'Center for Structural Genomics of Infectious Diseases' | 'Center for Structures of Membrane Proteins' | 'Center for the X-ray Structure Determination of Human Transporters' | 'Chaperone-Enabled Studies of Epigenetic Regulation Enzymes' | 'Enzyme Discovery for Natural Product Biosynthesis' | 'GPCR Network' | 'Integrated Center for Structure and Function Innovation' | 'Israel Structural Proteomics Center' | 'Joint Center for Structural Genomics' | 'Marseilles Structural Genomics Program @ AFMB' | 'Medical Structural Genomics of Pathogenic Protozoa' | 'Membrane Protein Structural Biology Consortium' | 'Membrane Protein Structures by Solution NMR' | 'Midwest Center for Macromolecular Research' | 'Midwest Center for Structural Genomics' | 'Mitochondrial Protein Partnership' | 'Montreal-Kingston Bacterial Structural Genomics Initiative' | 'Mycobacterium Tuberculosis Structural Proteomics Project' | 'New York Consortium on Membrane Protein Structure' | 'New York SGX Research Center for Structural Genomics' | 'New York Structural GenomiX Research Consortium' | 'New York Structural Genomics Research Consortium' | 'Northeast Structural Genomics Consortium' | 'Nucleocytoplasmic Transport: a Target for Cellular Control' | 'Ontario Centre for Structural Proteomics' | 'Oxford Protein Production Facility' | 'Paris-Sud Yeast Structural Genomics' | 'Partnership for Nuclear Receptor Signaling Code Biology' | 'Partnership for Stem Cell Biology' | 'Partnership for T-Cell Biology' | 'Program for the Characterization of Secreted Effector Proteins' | 'Protein Structure Factory' | 'RIKEN Structural Genomics/Proteomics Initiative' | 'Scottish Structural Proteomics Facility' | 'Seattle Structural Genomics Center for Infectious Disease' | 'South Africa Structural Targets Annotation Database' | 'Southeast Collaboratory for Structural Genomics' | 'Structural Genomics Consortium' | 'Structural Genomics Consortium for Research on Gene Expression' | 'Structural Genomics of Pathogenic Protozoa Consortium' | 'Structural Proteomics in Europe' | 'Structural Proteomics in Europe 2' | 'Structure 2 Function Project' | 'Structure, Dynamics and Activation Mechanisms of Chemokine Receptors' | 'Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes' | 'Structure-Function Studies of Tight Junction Membrane Proteins' | 'Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors' | 'TB Structural Genomics Consortium' | 'Transcontinental EM Initiative for Membrane Protein Structure' | 'Transmembrane Protein Center': The value identifies the full name of center. - `id` 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10, required: A unique integer identifier for this center - `initial_of_center` 'ATCG3D' | 'BIGS' | 'BSGC' | 'BSGI' | 'CEBS' | 'CELLMAT' | 'CESG' | 'CHSAM' | 'CHTSB' | 'CSBID' | 'CSGID' | 'CSMP' | 'GPCR' | 'IFN' | 'ISFI' | 'ISPC' | 'JCSG' | 'MCMR' | 'MCSG' | 'MPID' | 'MPP' | 'MPSBC' | 'MPSbyNMR' | 'MSGP' | 'MSGPP' | 'MTBI' | 'NESG' | 'NHRs' | 'NPCXstals' | 'NYCOMPS' | 'NYSGRC' | 'NYSGXRC' | 'NatPro' | 'OCSP' | 'OPPF' | 'PCSEP' | 'PSF' | 'RSGI' | 'S2F' | 'SASTAD' | 'SECSG' | 'SGC' | 'SGCGES' | 'SGPP' | 'SPINE' | 'SPINE-2' | 'SSGCID' | 'SSPF' | 'STEMCELL' | 'TBSGC' | 'TCELL' | 'TEMIMPS' | 'TJMP' | 'TMPC' | 'TransportPDB' | 'UC4CDI' | 'XMTB' | 'YSG': The value identifies the full name of center. - `project_name` 'Enzyme Function Initiative' | 'NIAID, National Institute of Allergy and Infectious Diseases' | 'NPPSFA, National Project on Protein Structural and Functional Analyses' | 'PSI, Protein Structure Initiative' | 'PSI:Biology': The value identifies the Structural Genomics project. - `pdbx_audit_revision_category` PdbxAuditRevisionCategory[] - `category` string: The category updated in the pdbx_audit_revision_category record. - `data_content_type` 'Additional map' | 'Chemical component' | 'EM metadata' | 'FSC' | 'Half map' | 'Image' | 'Mask' | 'NMR restraints' | 'NMR shifts' | 'Primary map' | 'Structure factors' | 'Structure model', required: The type of file that the pdbx_audit_revision_history record refers to. - `ordinal` integer, required: A unique identifier for the pdbx_audit_revision_category record. - `revision_ordinal` integer, required: A pointer to _pdbx_audit_revision_history.ordinal - `pdbx_audit_revision_details` PdbxAuditRevisionDetails[] - `data_content_type` 'Additional map' | 'Chemical component' | 'EM metadata' | 'FSC' | 'Half map' | 'Image' | 'Mask' | 'NMR restraints' | 'NMR shifts' | 'Primary map' | 'Structure factors' | 'Structure model', required: The type of file that the pdbx_audit_revision_history record refers to. - `description` string: Additional details describing the revision. - `details` string: Further details describing the revision. - `ordinal` integer, required: A unique identifier for the pdbx_audit_revision_details record. - `provider` 'author' | 'repository': The provider of the revision. - `revision_ordinal` integer, required: A pointer to _pdbx_audit_revision_history.ordinal - `type` 'Coordinate replacement' | 'Data added' | 'Data removed' | 'Data updated' | 'Initial release' | 'Obsolete' | 'Remediation': A type classification of the revision - `pdbx_audit_revision_group` PdbxAuditRevisionGroup[] - `data_content_type` 'Additional map' | 'Chemical component' | 'EM metadata' | 'FSC' | 'Half map' | 'Image' | 'Mask' | 'NMR restraints' | 'NMR shifts' | 'Primary map' | 'Structure factors' | 'Structure model', required: The type of file that the pdbx_audit_revision_history record refers to. - `group` 'Advisory' | 'Atomic model' | 'Author supporting evidence' | 'Data collection' | 'Data processing' | 'Database references' | 'Derived calculations' | 'Experimental data' | 'Experimental preparation' | 'Experimental summary' | 'Non-polymer description' | 'Other' | 'Polymer sequence' | 'Refinement description' | 'Source and taxonomy' | 'Structure summary' | 'Version format compliance': The collection of categories updated with this revision. - `ordinal` integer, required: A unique identifier for the pdbx_audit_revision_group record. - `revision_ordinal` integer, required: A pointer to _pdbx_audit_revision_history.ordinal - `pdbx_audit_revision_history` PdbxAuditRevisionHistory[] - `data_content_type` 'Additional map' | 'Chemical component' | 'EM metadata' | 'FSC' | 'Half map' | 'Image' | 'Mask' | 'NMR restraints' | 'NMR shifts' | 'Primary map' | 'Structure factors' | 'Structure model', required: The type of file that the pdbx_audit_revision_history record refers to. - `major_revision` integer: The major version number of deposition release. - `minor_revision` integer: The minor version number of deposition release. - `ordinal` integer, required: A unique identifier for the pdbx_audit_revision_history record. - `revision_date` string, date-time: The release date of the revision - `pdbx_audit_revision_item` PdbxAuditRevisionItem[] - `data_content_type` 'Additional map' | 'Chemical component' | 'EM metadata' | 'FSC' | 'Half map' | 'Image' | 'Mask' | 'NMR restraints' | 'NMR shifts' | 'Primary map' | 'Structure factors' | 'Structure model', required: The type of file that the pdbx_audit_revision_history record refers to. - `item` string: A high level explanation the author has provided for submitting a revision. - `ordinal` integer, required: A unique identifier for the pdbx_audit_revision_item record. - `revision_ordinal` integer, required: A pointer to _pdbx_audit_revision_history.ordinal - `pdbx_audit_support` PdbxAuditSupport[] - `country` string: The country/region providing the funding support for the entry. Funding information is optionally provided for entries after June 2016. - `funding_organization` string: The name of the organization providing funding support for the entry. Funding information is optionally provided for entries after June 2016. - `grant_number` string: The grant number associated with this source of support. - `ordinal` integer, required: A unique sequential integer identifier for each source of support for this entry. - `pdbx_database_PDB_obs_spr` PdbxDatabasePDBObsSpr[] - `date` string, date-time: The date of replacement. - `details` string: Details related to the replaced or replacing entry. - `id` 'OBSLTE' | 'SPRSDE': Identifier for the type of obsolete entry to be added to this entry. - `pdb_id` string, required: The new PDB identifier for the replaced entry. - `replace_pdb_id` string, required: The PDB identifier for the replaced (OLD) entry/entries. - `pdbx_database_related` PdbxDatabaseRelated[] - `content_type` 'associated EM volume' | 'associated NMR restraints' | 'associated SAS data' | 'associated structure factors' | 'complete structure' | 'consensus EM volume' | 'derivative structure' | 'ensemble' | 'focused EM volume' | 'minimized average structure' | 'native structure' | 'other' | 'other EM volume' | 'protein target sequence and/or protocol data' | 're-refinement' | 'representative structure' | 'split' | 'unspecified', required: The identifying content type of the related entry. - `db_id` string, required: The identifying code in the related database. - `db_name` 'BIOISIS' | 'BMCD' | 'BMRB' | 'EMDB' | 'NDB' | 'PDB' | 'PDB-Dev' | 'SASBDB' | 'TargetDB' | 'TargetTrack', required: The name of the database containing the related entry. - `details` string: A description of the related entry. - `pdbx_database_status` PdbxDatabaseStatus - `SG_entry` 'N' | 'Y': This code indicates whether the entry belongs to Structural Genomics Project. - `deposit_site` 'BMRB' | 'BNL' | 'NDB' | 'PDBC' | 'PDBE' | 'PDBJ' | 'RCSB': The site where the file was deposited. - `methods_development_category` 'CAPRI' | 'CASD-NMR' | 'CASP' | 'D3R' | 'FoldIt' | 'GPCR Dock' | 'RNA-Puzzles': The methods development category in which this entry has been placed. - `pdb_format_compatible` 'N' | 'Y': A flag indicating that the entry is compatible with the PDB format. A value of 'N' indicates that the no PDB format data file is corresponding to this entry is available in the PDB archive. - `process_site` 'BNL' | 'NDB' | 'PDBC' | 'PDBE' | 'PDBJ' | 'RCSB': The site where the file was deposited. - `recvd_initial_deposition_date` string, date-time: The date of initial deposition. (The first message for deposition has been received.) - `status_code` 'AUCO' | 'AUTH' | 'BIB' | 'DEL' | 'HOLD' | 'HPUB' | 'OBS' | 'POLC' | 'PROC' | 'REFI' | 'REL' | 'REPL' | 'REV' | 'RMVD' | 'TRSF' | 'UPD' | 'WAIT' | 'WDRN': Code for status of file. - `status_code_cs` 'AUCO' | 'AUTH' | 'HOLD' | 'HPUB' | 'OBS' | 'POLC' | 'PROC' | 'REL' | 'REPL' | 'RMVD' | 'WAIT' | 'WDRN': Code for status of chemical shift data file. - `status_code_mr` 'AUCO' | 'AUTH' | 'HOLD' | 'HPUB' | 'OBS' | 'POLC' | 'PROC' | 'REL' | 'REPL' | 'RMVD' | 'WAIT' | 'WDRN': Code for status of NMR constraints file. - `status_code_sf` 'AUTH' | 'HOLD' | 'HPUB' | 'OBS' | 'POLC' | 'PROC' | 'REL' | 'REPL' | 'RMVD' | 'WAIT' | 'WDRN': Code for status of structure factor file. - `pdbx_deposit_group` PdbxDepositGroup[] - `group_description` string: A description of the contents of entries in the collection. - `group_id` string, required: A unique identifier for a group of entries deposited as a collection. - `group_title` string: A title to describe the group of entries deposited in the collection. - `group_type` 'changed state' | 'ground state' | 'undefined': Text to describe a grouping of entries in multiple collections - `pdbx_initial_refinement_model` PdbxInitialRefinementModel[] - `accession_code` string: This item identifies an accession code of the resource where the initial model is used - `details` string: A description of special aspects of the initial model - `entity_id_list` string[]: A comma separated list of entities reflecting the initial model used for refinement - `id` integer, required: A unique identifier for the starting model record. - `source_name` 'AlphaFold' | 'ITasser' | 'InsightII' | 'ModelAngelo' | 'ModelArchive' | 'Modeller' | 'Other' | 'PDB' | 'PDB-Dev' | 'PHYRE' | 'Robetta' | 'RoseTTAFold' | 'SwissModel': This item identifies the resource of initial model used for refinement - `type` 'experimental model' | 'in silico model' | 'integrative model' | 'other': This item describes the type of the initial model was generated - `pdbx_molecule_features` PdbxMoleculeFeatures[] - `class` 'Antagonist' | 'Anthelmintic' | 'Antibiotic' | 'Antibiotic, Anthelmintic' | 'Antibiotic, Antimicrobial' | 'Antibiotic, Antineoplastic' | 'Anticancer' | 'Anticoagulant' | 'Anticoagulant, Antithrombotic' | 'Antifungal' | 'Antigen' | 'Antiinflammatory' | 'Antimicrobial' | 'Antimicrobial, Antiparasitic, Antibiotic' | 'Antimicrobial, Antiretroviral' | 'Antimicrobial, Antitumor' | 'Antineoplastic' | 'Antiparasitic' | 'Antiretroviral' | 'Antithrombotic' | 'Antitumor' | 'Antiviral' | 'CASPASE inhibitor' | 'Chaperone binding' | 'Drug delivery' | 'Enzyme inhibitor' | 'Glycan component' | 'Growth factor' | 'Immunosuppressant' | 'Inducer' | 'Inhibitor' | 'Lantibiotic' | 'Metabolism' | 'Metal transport' | 'Nutrient' | 'Oxidation-reduction' | 'Protein binding' | 'Receptor' | 'Substrate analog' | 'Synthetic opioid' | 'Thrombin inhibitor' | 'Thrombin inhibitor, Trypsin inhibitor' | 'Toxin' | 'Transition state mimetic' | 'Transport activator' | 'Trypsin inhibitor' | 'Unknown' | 'Water retention': Broadly defines the function of the molecule. - `details` string: Additional details describing the molecule. - `name` string: A name of the molecule. - `prd_id` string, required: The value of _pdbx_molecule_features.prd_id is the accession code for this reference molecule. - `type` 'Amino acid' | 'Aminoglycoside' | 'Ansamycin' | 'Anthracycline' | 'Anthraquinone' | 'Chalkophore' | 'Chalkophore, Polypeptide' | 'Chromophore' | 'Cyclic depsipeptide' | 'Cyclic lipopeptide' | 'Cyclic peptide' | 'Glycopeptide' | 'Heterocyclic' | 'Imino sugar' | 'Keto acid' | 'Lipoglycopeptide' | 'Lipopeptide' | 'Macrolide' | 'Non-polymer' | 'Nucleoside' | 'Oligopeptide' | 'Oligosaccharide' | 'Peptaibol' | 'Peptide-like' | 'Polycyclic' | 'Polypeptide' | 'Polysaccharide' | 'Quinolone' | 'Siderophore' | 'Thiolactone' | 'Thiopeptide' | 'Unknown': Defines the structural classification of the molecule. - `pdbx_nmr_details` PdbxNmrDetails - `text` string: Additional details describing the NMR experiment. - `pdbx_nmr_ensemble` PdbxNmrEnsemble - `average_constraint_violations_per_residue` integer: The average number of constraint violations on a per residue basis for the ensemble. - `average_constraints_per_residue` integer: The average number of constraints per residue for the ensemble - `average_distance_constraint_violation` number, double: The average distance restraint violation for the ensemble. - `average_torsion_angle_constraint_violation` number, double: The average torsion angle constraint violation for the ensemble. - `conformer_selection_criteria` string: By highlighting the appropriate choice(s), describe how the submitted conformer (models) were selected. - `conformers_calculated_total_number` integer: The total number of conformer (models) that were calculated in the final round. - `conformers_submitted_total_number` integer: The number of conformer (models) that are submitted for the ensemble. - `distance_constraint_violation_method` string: Describe the method used to calculate the distance constraint violation statistics, i.e. are they calculated over all the distance constraints or calculated for violations only? - `maximum_distance_constraint_violation` number, double: The maximum distance constraint violation for the ensemble. - `maximum_lower_distance_constraint_violation` number, double: The maximum lower distance constraint violation for the ensemble. - `maximum_torsion_angle_constraint_violation` number, double: The maximum torsion angle constraint violation for the ensemble. - `maximum_upper_distance_constraint_violation` number, double: The maximum upper distance constraint violation for the ensemble. - `representative_conformer` integer: The number of the conformer identified as most representative. - `torsion_angle_constraint_violation_method` string: This item describes the method used to calculate the torsion angle constraint violation statistics. i.e. are the entered values based on all torsion angle or calculated for violations only? - `pdbx_nmr_exptl` PdbxNmrExptl[] - `conditions_id` string, required: The number to identify the set of sample conditions. - `experiment_id` string, required: A numerical ID for each experiment. - `sample_state` 'anisotropic' | 'isotropic': Physical state of the sample either anisotropic or isotropic. - `solution_id` string, required: The solution_id from the Experimental Sample to identify the sample that these conditions refer to. [Remember to save the entries here before returning to the Experimental Sample form] - `spectrometer_id` integer: Pointer to '_pdbx_nmr_spectrometer.spectrometer_id' - `type` string: The type of NMR experiment. - `pdbx_nmr_exptl_sample_conditions` PdbxNmrExptlSampleConditions[] - `conditions_id` string, required: The condition number as defined above. - `details` string: General details describing conditions of both the sample and the environment during measurements. - `ionic_strength` string: The ionic strength at which the NMR data were collected -in lieu of this enter the concentration and identity of the salt in the sample. - `ionic_strength_err` number, double: Estimate of the standard error for the value for the sample ionic strength. - `ionic_strength_units` 'M' | 'Not defined' | 'mM': Units for the value of the sample condition ionic strength.. - `label` string: A descriptive label that uniquely identifies this set of sample conditions. - `pH` string: The pH at which the NMR data were collected. - `pH_err` number, double: Estimate of the standard error for the value for the sample pH. - `pH_units` 'Not defined' | 'pD' | 'pH' | 'pH*': Units for the value of the sample condition pH. - `pressure` string: The pressure at which NMR data were collected. - `pressure_err` number, double: Estimate of the standard error for the value for the sample pressure. - `pressure_units` string: The units of pressure at which NMR data were collected. - `temperature` string: The temperature (in kelvin) at which NMR data were collected. - `temperature_err` number, double: Estimate of the standard error for the value for the sample temperature. - `temperature_units` 'C' | 'K' | 'Not defined': Units for the value of the sample condition temperature. - `pdbx_nmr_refine` PdbxNmrRefine[] - `details` string: Additional details about the NMR refinement. - `method` string: The method used to determine the structure. - `software_ordinal` integer, required: Pointer to _software.ordinal - `pdbx_nmr_representative` PdbxNmrRepresentative - `conformer_id` string: If a member of the ensemble has been selected as a representative structure, identify it by its model number. - `selection_criteria` string: By highlighting the appropriate choice(s), describe the criteria used to select this structure as a representative structure, or if an average structure has been calculated describe how this was done. - `pdbx_nmr_sample_details` PdbxNmrSampleDetails[] - `contents` string: A complete description of each NMR sample. Include the concentration and concentration units for each component (include buffers, etc.). For each component describe the isotopic composition, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labeled biomolecule is designated by NA: U-13C; NA-K,H - `details` string: Brief description of the sample providing additional information not captured by other items in the category. - `label` string: A value that uniquely identifies this sample from the other samples listed in the entry. - `solution_id` string, required: The name (number) of the sample. - `solvent_system` string: The solvent system used for this sample. - `type` 'bicelle' | 'emulsion' | 'fiber' | 'fibrous protein' | 'filamentous virus' | 'gel solid' | 'gel solution' | 'liposome' | 'lyophilized powder' | 'membrane' | 'micelle' | 'oriented membrane film' | 'polycrystalline powder' | 'reverse micelle' | 'single crystal' | 'solid' | 'solution': A descriptive term for the sample that defines the general physical properties of the sample. - `pdbx_nmr_software` PdbxNmrSoftware[] - `authors` string: The name of the authors of the software used in this procedure. - `classification` string: The purpose of the software. - `name` string: The name of the software used for the task. - `ordinal` integer, required: An ordinal index for this category - `version` string: The version of the software. - `pdbx_nmr_spectrometer` PdbxNmrSpectrometer[] - `details` string: A text description of the NMR spectrometer. - `field_strength` number, double: The field strength in MHz of the spectrometer - `manufacturer` string: The name of the manufacturer of the spectrometer. - `model` string: The model of the NMR spectrometer. - `spectrometer_id` string, required: Assign a numerical ID to each instrument. - `type` string: Select the instrument manufacturer(s) and the model(s) of the NMR(s) used for this work. - `pdbx_reflns_twin` PdbxReflnsTwin[] - `crystal_id` string, required: The crystal identifier. A reference to _exptl_crystal.id in category EXPTL_CRYSTAL. - `diffrn_id` string, required: The diffraction data set identifier. A reference to _diffrn.id in category DIFFRN. - `domain_id` string: An identifier for the twin domain. - `fraction` number, double: The twin fraction or twin factor represents a quantitative parameter for the crystal twinning. The value 0 represents no twinning, < 0.5 partial twinning, = 0.5 for perfect twinning. - `operator` string, required: The possible merohedral or hemihedral twinning operators for different point groups are: True point group Twin operation hkl related to 3 2 along a,b h,-h-k,-l 2 along a*,b* h+k,-k,-l 2 along c -h,-k,l 4 2 along a,b,a*,b* h,-k,-l 6 2 along a,b,a*,b* h,-h-k,-l 321 2 along a*,b*,c -h,-k,l 312 2 along a,b,c -h,-k,l 23 4 along a,b,c k,-h,l References: Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and Overcoming Crystal Twinning. and information from the following on-line sites: CNS site http://cns.csb.yale.edu/v1.1/ CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html - `type` 'epitaxial' | 'hemihedral' | 'merohedral' | 'non-merohedral' | 'pseudo-merohedral' | 'tetartohedral': There are two types of twinning: merohedral or hemihedral non-merohedral or epitaxial For merohedral twinning the diffraction patterns from the different domains are completely superimposable. Hemihedral twinning is a special case of merohedral twinning. It only involves two distinct domains. Pseudo-merohedral twinning is a subclass merohedral twinning in which lattice is coincidentally superimposable. In the case of non-merohedral or epitaxial twinning the reciprocal lattices do not superimpose exactly. In this case the diffraction pattern consists of two (or more) interpenetrating lattices, which can in principle be separated. - `pdbx_related_exp_data_set` PdbxRelatedExpDataSet[] - `data_reference` string: A DOI reference to the related data set. - `data_set_type` string: The type of the experimenatal data set. - `db_source` 'Apollo - University of Cambridge Repository' | 'CXIDB' | 'DRYAD Database' | 'EMPIAR' | 'ESRF Data Portal' | 'ETH Zurich Research Collection' | 'Etsin' | 'Integrated Resource for Reproducibility in Macromolecular Crystallography' | 'International Union of Crystallography' | 'KAUST Repository' | 'Keele Data Repository' | 'MAXIV Public Data Repository' | 'MX-RDR (Macromolecular Xtallography Raw Data Repository)' | 'Manchester eScholar Services' | 'Mendeley Data' | 'PSI Public Data Repository' | 'ProteinDiffraction' | 'RMIT University Figshare' | 'SBGrid Data Bank' | 'Xtal Raw Data Archive' | 'Zenodo': For external sources, the name of the resource. - `details` string: Additional details describing the content of the related data set and its application to the current investigation. - `metadata_reference` string: A DOI reference to the metadata decribing the related data set. - `pdbx_serial_crystallography_data_reduction` PdbxSerialCrystallographyDataReduction[] - `crystal_hits` integer: For experiments in which samples are provided in a continuous stream, the total number of frames collected in which the crystal was hit. - `diffrn_id` string, required: The data item is a pointer to _diffrn.id in the DIFFRN category. - `droplet_hits` integer: For experiments in which samples are provided in a continuous stream, the total number of frames collected in which a droplet was hit. - `frame_hits` integer: For experiments in which samples are provided in a continuous stream, the total number of data frames collected in which the sample was hit. - `frames_failed_index` integer: For experiments in which samples are provided in a continuous stream, the total number of data frames collected that contained a "hit" but failed to index. - `frames_indexed` integer: For experiments in which samples are provided in a continuous stream, the total number of data frames collected that were indexed. - `frames_total` integer: The total number of data frames collected for this data set. - `lattices_indexed` integer: For experiments in which samples are provided in a continuous stream, the total number of lattices indexed. - `lattices_merged` integer: For experiments in which samples are provided in a continuous stream, the total number of crystal lattices that were merged in the final dataset. Can be less than frames_indexed depending on filtering during merging or can be more than frames_indexed if there are multiple lattices. per frame. - `xfel_pulse_events` integer: For FEL experiments, the number of pulse events in the dataset. - `xfel_run_numbers` string: For FEL experiments, in which data collection was performed in batches, indicates which subset of the data collected were used in producing this dataset. - `pdbx_serial_crystallography_measurement` PdbxSerialCrystallographyMeasurement[] - `collection_time_total` number, double: The total number of hours required to measure this data set. - `collimation` string: The collimation or type of focusing optics applied to the radiation. - `diffrn_id` string, required: The data item is a pointer to _diffrn.id in the DIFFRN category. - `focal_spot_size` number, double: The focal spot size of the beam impinging on the sample (micrometres squared). - `photons_per_pulse` number, double: The photons per pulse measured in (tera photons (10^(12)^)/pulse units). - `pulse_duration` number, double: The average duration (femtoseconds) of the pulse energy measured at the sample. - `pulse_energy` number, double: The energy/pulse of the X-ray pulse impacting the sample measured in microjoules. - `pulse_photon_energy` number, double: The photon energy of the X-ray pulse measured in KeV. - `source_distance` number, double: The distance from source to the sample along the optical axis (metres). - `source_size` number, double: The dimension of the source beam measured at the source (micrometres squared). - `xfel_pulse_repetition_rate` number, double: For FEL experiments, the pulse repetition rate measured in cycles per seconds. - `pdbx_serial_crystallography_sample_delivery` PdbxSerialCrystallographySampleDelivery[] - `description` string: The description of the mechanism by which the specimen in placed in the path of the source. - `diffrn_id` string, required: The data item is a pointer to _diffrn.id in the DIFFRN category. - `method` 'fixed target' | 'injection' | 'other': The description of the mechanism by which the specimen in placed in the path of the source. - `pdbx_serial_crystallography_sample_delivery_fixed_target` PdbxSerialCrystallographySampleDeliveryFixedTarget[] - `crystals_per_unit` integer: The number of crystals per dropplet or pore in fixed target - `description` string: For a fixed target sample, a description of sample preparation - `details` string: Any details pertinent to the fixed sample target - `diffrn_id` string, required: The data item is a pointer to _diffrn.id in the DIFFRN category. - `motion_control` string: Device used to control movement of the fixed sample - `sample_dehydration_prevention` string: Method to prevent dehydration of sample - `sample_holding` string: For a fixed target sample, mechanism to hold sample in the beam - `sample_solvent` string: The sample solution content and concentration - `sample_unit_size` number, double: Size of pore in grid supporting sample. Diameter or length in micrometres, e.g. pore diameter - `support_base` string: Type of base holding the support - `velocity_horizontal` number, double: Velocity of sample horizontally relative to a perpendicular beam in millimetres/second - `velocity_vertical` number, double: Velocity of sample vertically relative to a perpendicular beam in millimetres/second - `pdbx_serial_crystallography_sample_delivery_injection` PdbxSerialCrystallographySampleDeliveryInjection[] - `carrier_solvent` string: For continuous sample flow experiments, the carrier buffer used to move the sample into the beam. Should include protein concentration. - `crystal_concentration` number, double: For continuous sample flow experiments, the concentration of crystals in the solution being injected. The concentration is measured in million crystals/ml. - `description` string: For continuous sample flow experiments, a description of the injector used to move the sample into the beam. - `diffrn_id` string, required: The data item is a pointer to _diffrn.id in the DIFFRN category. - `filter_size` number, double: The size of filter in micrometres in filtering crystals - `flow_rate` number, double: For continuous sample flow experiments, the flow rate of solution being injected measured in ul/min. - `injector_diameter` number, double: For continuous sample flow experiments, the diameter of the injector in micrometres. - `injector_nozzle` string: The type of nozzle to deliver and focus sample jet - `injector_pressure` number, double: For continuous sample flow experiments, the mean pressure in kilopascals at which the sample is injected into the beam. - `injector_temperature` number, double: For continuous sample flow experiments, the temperature in Kelvins of the speciman injected. This may be different from the temperature of the sample. - `jet_diameter` number, double: Diameter in micrometres of jet stream of sample delivery - `power_by` string: Sample deliver driving force, e.g. Gas, Electronic Potential - `preparation` string: Details of crystal growth and preparation of the crystals - `pdbx_soln_scatter` PdbxSolnScatter[] - `buffer_name` string: The name of the buffer used for the sample in the solution scattering experiment. - `concentration_range` string: The concentration range (mg/mL) of the complex in the sample used in the solution scattering experiment to determine the mean radius of structural elongation. - `data_analysis_software_list` string: A list of the software used in the data analysis - `data_reduction_software_list` string: A list of the software used in the data reduction - `detector_specific` string: The particular radiation detector. In general this will be a manufacturer, description, model number or some combination of these. - `detector_type` string: The general class of the radiation detector. - `id` string, required: The value of _pdbx_soln_scatter.id must uniquely identify the sample in the category PDBX_SOLN_SCATTER - `max_mean_cross_sectional_radii_gyration` number, double: The maximum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 - `max_mean_cross_sectional_radii_gyration_esd` number, double: The estimated standard deviation for the minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 - `mean_guiner_radius` number, double: The mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q gives the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 - `mean_guiner_radius_esd` number, double: The estimated standard deviation for the mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 - `min_mean_cross_sectional_radii_gyration` number, double: The minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 - `min_mean_cross_sectional_radii_gyration_esd` number, double: The estimated standard deviation for the minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 - `num_time_frames` integer: The number of time frame solution scattering images used. - `protein_length` string: The length (or range) of the protein sample under study. If the solution structure is approximated as an elongated elliptical cyclinder the length L is determined from, L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ] The length should also be given by L = pi I(0) / [ I(Q).Q]_Q->0 - `sample_pH` number, double: The pH value of the buffered sample. - `source_beamline` string: The beamline name used for the experiment - `source_beamline_instrument` string: The instrumentation used on the beamline - `source_class` string: The general class of the radiation source. - `source_type` string: The make, model, name or beamline of the source of radiation. - `temperature` number, double: The temperature in kelvins at which the experiment was conducted - `type` 'modelling' | 'neutron' | 'x-ray': The type of solution scattering experiment carried out - `pdbx_soln_scatter_model` PdbxSolnScatterModel[] - `conformer_selection_criteria` string: A description of the conformer selection criteria used. - `details` string: A description of any additional details concerning the experiment. - `entry_fitting_list` string: A list of the entries used to fit the model to the scattering data - `id` string, required: The value of _pdbx_soln_scatter_model.id must uniquely identify the sample in the category PDBX_SOLN_SCATTER_MODEL - `method` string: A description of the methods used in the modelling - `num_conformers_calculated` integer: The number of model conformers calculated. - `num_conformers_submitted` integer: The number of model conformers submitted in the entry - `representative_conformer` integer: The index of the representative conformer among the submitted conformers for the entry - `scatter_id` string, required: This data item is a pointer to _pdbx_soln_scatter.id in the PDBX_SOLN_SCATTER category. - `software_author_list` string: A list of the software authors - `software_list` string: A list of the software used in the modeeling - `pdbx_vrpt_summary` PdbxVrptSummary - `RNA_suiteness` number, double: The MolProbity conformer-match quality parameter for RNA structures. Low values are worse. Specific to structures that contain RNA polymers. - `attempted_validation_steps` string: The steps that were attempted by the validation pipeline software. A step typically involves running a 3rd party validation tool, for instance "mogul" Each step will be enumerated in _pdbx_vrpt_software category. - `ligands_for_buster_report` 'N' | 'Y': A flag indicating if there are ligands in the model used for detailed Buster analysis. - `report_creation_date` string, date-time: The date, time and time-zone that the validation report was created. The string will be formatted like yyyy-mm-dd:hh:mm in GMT time. - `restypes_notchecked_for_bond_angle_geometry` string[]: This is a comma separated list of the residue types whose bond lengths and bond angles have not been checked against "standard geometry" using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996) - `pdbx_vrpt_summary_diffraction` PdbxVrptSummaryDiffraction[] - `B_factor_type` 'FULL' | 'PARTIAL': An indicator if isotropic B factors are partial or full values. - `Babinet_b` number, double: REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'. X-ray entry specific, obtained in the EDS step from REFMAC calculation. - `Babinet_k` number, double: REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'. X-ray entry specific, obtained in the EDS step from REFMAC calculation. - `CCP4_version` string: The version of CCP4 suite used in the analysis. - `DCC_R` number, double: The overall R-factor from a DCC recalculation of an electron density map. Currently value is rounded to 2 decimal places. X-ray entry specific, obtained from the DCC program. - `DCC_Rfree` number, double: Rfree as calculated by DCC. - `EDS_R` number, double: The overall R factor from the EDS REFMAC calculation (no free set is used in this). Currently value is rounded to 2 decimal places. X-ray entry specific, obtained in the eds step from REFMAC calculation. - `EDS_R_warning` string: Warning message when EDS calculated R vs reported R is higher than a threshold - `EDS_res_high` number, double: The data high resolution diffraction limit, in Angstroms, found in the input structure factor file. X-ray entry specific, obtained in the EDS step. - `EDS_res_low` number, double: The data low resolution diffraction limit, in Angstroms, found in the input structure factor file. X-ray entry specific, obtained in the EDS step. - `Fo_Fc_correlation` number, double: Fo,Fc correlation: The difference between the observed structure factors (Fo) and the calculated structure factors (Fc) measures the correlation between the model and the experimental data. X-ray entry specific, obtained in the eds step from REFMAC calculation. - `I_over_sigma` string: Each reflection has an intensity (I) and an uncertainty in measurement (sigma(I)), so I/sigma(I) is the signal-to-noise ratio. This ratio decreases at higher resolution. is the mean of individual I/sigma(I) values. Value for outer resolution shell is given in parentheses. In case structure factor amplitudes are deposited, Xtriage estimates the intensities first and then calculates this metric. When intensities are available in the deposited file, these are converted to amplitudes and then back to intensity estimate before calculating the metric. X-ray entry specific, calculated by Phenix Xtriage program. - `Padilla_Yeates_L2_mean` number, double: Padilla and Yeates twinning parameter <|L**2|>. Theoretical values is 0.333 in the untwinned case, and 0.2 in the perfectly twinned case. X-ray entry specific, obtained from the Xtriage program. - `Padilla_Yeates_L_mean` number, double: Padilla and Yeates twinning parameter <|L|>. Theoretical values is 0.5 in the untwinned case, and 0.375 in the perfectly twinned case. X-ray entry specific, obtained from the Xtriage program. - `Q_score` number, double: The overall Q-score of the fit of coordinates to the electron map. The Q-score is defined in Pintilie, GH. et al., Nature Methods, 17, 328-334 (2020) - `Wilson_B_aniso` string: Result of absolute likelihood based Wilson scaling, The anisotropic B value of the data is determined using a likelihood based approach. The resulting B tensor is reported, the 3 diagonal values are given first, followed by the 3 off diagonal values. A large spread in (especially the diagonal) values indicates anisotropy. X-ray entry specific, calculated by Phenix Xtriage program. - `Wilson_B_estimate` number, double: An estimate of the overall B-value of the structure, calculated from the diffraction data. Units Angstroms squared. It serves as an indicator of the degree of order in the crystal and the value is usually not hugely different from the average B-value calculated from the model. X-ray entry specific, calculated by Phenix Xtriage program. - `acentric_outliers` integer: The number of acentric reflections that Xtriage identifies as outliers on the basis of Wilson statistics. Note that if pseudo translational symmetry is present, a large number of 'outliers' will be present. X-ray entry specific, calculated by Phenix Xtriage program. - `bulk_solvent_b` number, double: REFMAC scaling parameter as reported in log output file. X-ray entry specific, obtained in the EDS step from REFMAC calculation. - `bulk_solvent_k` number, double: REFMAC reported scaling parameter. X-ray entry specific, obtained in the EDS step from REFMAC calculation. - `centric_outliers` integer: The number of centric reflections that Xtriage identifies as outliers. X-ray entry specific, calculated by Phenix Xtriage program. - `data_anisotropy` number, double: The ratio (Bmax - Bmin) / Bmean where Bmax, Bmin and Bmean are computed from the B-values associated with the principal axes of the anisotropic thermal ellipsoid. This ratio is usually less than 0.5; for only 1% of PDB entries it is more than 1.0 (Read et al., 2011). X-ray entry specific, obtained from the Xtriage program. - `data_completeness` number, double: The percent completeness of diffraction data. - `density_fitness_version` string: The version of density-fitness suite programs used in the analysis. - `exp_method` string: Experimental method for statistics - `num_miller_indices` integer: The number of Miller Indices reported by the Xtriage program. This should be the same as the number of _refln in the input structure factor file. X-ray entry specific, calculated by Phenix Xtriage program. - `number_reflns_R_free` integer: The number of reflections in the free set as defined in the input structure factor file supplied to the validation pipeline. X-ray entry specific, obtained from the DCC program. - `percent_RSRZ_outliers` number, double: The percent of RSRZ outliers. - `percent_free_reflections` number, double: A percentage, Normally percent proportion of the total number. Between 0% and 100%. - `servalcat_version` string: The version of Servalcat program used in the analysis. - `trans_NCS_details` string: A sentence giving the result of Xtriage's analysis on translational NCS. X-ray entry specific, obtained from the Xtriage program. - `twin_fraction` string: Estimated twinning fraction for operators as identified by Xtriage. A semicolon separated list of operators with fractions is givens X-ray entry specific, obtained from the Xtriage program. - `pdbx_vrpt_summary_em` PdbxVrptSummaryEm[] - `Q_score` number, double: The overall Q-score of the fit of coordinates to the electron map. The Q-score is defined in Pintilie, GH. et al., Nature Methods, 17, 328-334 (2020) - `atom_inclusion_all_atoms` number, double: The proportion of all non hydrogen atoms within density. - `atom_inclusion_backbone` number, double: The proportion of backbone atoms within density. - `author_provided_fsc_resolution_by_cutoff_halfbit` number, double: The resolution from the intersection of the author provided fsc and the indicator curve halfbit. - `author_provided_fsc_resolution_by_cutoff_onebit` number, double: The resolution from the intersection of the author provided fsc and the indicator curve onebit. - `author_provided_fsc_resolution_by_cutoff_pt_143` number, double: The resolution from the intersection of the author provided fsc and the indicator curve 0.143. - `author_provided_fsc_resolution_by_cutoff_pt_333` number, double: The resolution from the intersection of the author provided fsc and the indicator curve 0.333. - `author_provided_fsc_resolution_by_cutoff_pt_5` number, double: The resolution from the intersection of the author provided fsc and the indicator curve 0.5. - `author_provided_fsc_resolution_by_cutoff_threesigma` number, double: The resolution from the intersection of the author provided fsc and the indicator curve threesigma. - `calculated_fsc_resolution_by_cutoff_halfbit` number, double: The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve halfbit. - `calculated_fsc_resolution_by_cutoff_onebit` number, double: The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve onebit. - `calculated_fsc_resolution_by_cutoff_pt_143` number, double: The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.143. - `calculated_fsc_resolution_by_cutoff_pt_333` number, double: The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.333. - `calculated_fsc_resolution_by_cutoff_pt_5` number, double: The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.5. - `calculated_fsc_resolution_by_cutoff_threesigma` number, double: The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve threesigma. - `contour_level_primary_map` number, double: The recommended contour level for the primary map of this deposition. - `exp_method` string: Experimental method for statistics - `pdbx_vrpt_summary_geometry` PdbxVrptSummaryGeometry[] - `angles_RMSZ` number, double: The overall root mean square of the Z-score for deviations of bond angles in comparison to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). This value is for all chains in the structure. - `bonds_RMSZ` number, double: The overall root mean square of the Z-score for deviations of bond lengths in comparison to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). This value is for all chains in the structure. - `clashscore` number, double: This score is derived from the number of pairs of atoms in the PDB_model_num that are unusually close to each other. It is calculated by the MolProbity pdbx_vrpt_software and expressed as the number or such clashes per thousand atoms. For structures determined by NMR the clashscore value here will only consider label_atom_id pairs in the well-defined (core) residues from ensemble analysis. - `clashscore_full_length` number, double: Only given for structures determined by NMR. The MolProbity pdbx_vrpt_instance_clashes score for all label_atom_id pairs. - `num_H_reduce` integer: This is the number of hydrogen atoms added and optimized by the MolProbity reduce pdbx_vrpt_software as part of the all-atom clashscore. - `num_angles_RMSZ` integer: The number of bond angles compared to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). This value is for all chains in the structure. - `num_bonds_RMSZ` integer: The number of bond lengths compared to "standard geometry" made using the MolProbity dangle program. Standard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996). This value is for all chains in the structure. - `percent_ramachandran_outliers` number, double: The percentage of residues with Ramachandran outliers. - `percent_ramachandran_outliers_full_length` number, double: Only given for structures determined by NMR. The MolProbity Ramachandran outlier score for all atoms in the structure rather than just the well-defined (core) residues. - `percent_rotamer_outliers` number, double: The MolProbity sidechain outlier score (a percentage). Protein sidechains mostly adopt certain (combinations of) preferred torsion angle values (called rotamers or rotameric conformers), much like their backbone torsion angles (as assessed in the Ramachandran analysis). MolProbity considers the sidechain conformation of a residue to be an outlier if its set of torsion angles is not similar to any preferred combination. The sidechain outlier score is calculated as the percentage of residues with an unusual sidechain conformation with respect to the total number of residues for which the assessment is available. Example: percent-rota-outliers="2.44". Specific to structure that contain protein chains and have sidechains modelled. For NMR structures only the well-defined (core) residues from ensemble analysis will be considered. The percentage of residues with rotamer outliers. - `percent_rotamer_outliers_full_length` number, double: Only given for structures determined by NMR. The MolProbity sidechain outlier score for all atoms in the structure rather than just the well-defined (core) residues. - `pdbx_vrpt_summary_nmr` PdbxVrptSummaryNmr[] - `chemical_shift_completeness` number, double: Overall completeness of the chemical shift assignments for the well-defined regions of the structure. - `chemical_shift_completeness_full_length` number, double: Overall completeness of the chemical shift assignments for the full macromolecule or complex as suggested by the molecular description of an entry (whether some portion of it is modelled or not). - `cyrange_error` string: Diagnostic message from the wrapper of Cyrange software which identifies the well-defined cores (domains) of NMR protein structures. - `cyrange_number_of_domains` integer: Total number of well-defined cores (domains) identified by Cyrange - `exp_method` string: Experimental method for statistics - `medoid_model` integer: For each Cyrange well-defined core ("cyrange_domain") the id of the PDB_model_num which is most similar to other models as measured by pairwise RMSDs over the domain. For the whole entry ("Entry"), the medoid PDB_model_num of the largest core is taken as an overall representative of the structure. - `nmr_models_consistency_flag` string: A flag indicating if all models in the NMR ensemble contain the exact same atoms ("True") or if the models differ in this respect ("False"). - `nmrclust_error` string: Diagnostic message from the wrapper of NMRClust software which clusters NMR models. - `nmrclust_number_of_clusters` integer: Total number of clusters in the NMR ensemble identified by NMRClust. - `nmrclust_number_of_models` integer: Number of models analysed by NMRClust - should in almost all cases be the same as the number of models in the NMR ensemble. - `nmrclust_number_of_outliers` integer: Number of models that do not belong to any cluster as deemed by NMRClust. - `nmrclust_representative_model` integer: Overall representative PDB_model_num of the NMR ensemble as identified by NMRClust. - `rcsb_accession_info` RcsbAccessionInfo - `deposit_date` string, date-time: The entry deposition date. - `has_released_experimental_data` 'N' | 'Y': A code indicating the current availibility of experimental data in the repository. - `initial_release_date` string, date-time: The entry initial release date. - `major_revision` integer: The latest entry major revision number. - `minor_revision` integer: The latest entry minor revision number. - `revision_date` string, date-time: The latest entry revision date. - `status_code` 'AUCO' | 'AUTH' | 'HOLD' | 'HPUB' | 'POLC' | 'PROC' | 'REFI' | 'REL' | 'REPL' | 'WAIT' | 'WDRN': The release status for the entry. - `rcsb_binding_affinity` RcsbBindingAffinity[] - `comp_id` string, required: Ligand identifier. - `link` string, required: Link to external resource referencing the data. - `provenance_code` 'Binding MOAD' | 'BindingDB' | 'PDBBind', required: The resource name for the related binding affinity reference. - `reference_sequence_identity` integer: Data point provided by BindingDB. Percent identity between PDB sequence and reference sequence. - `symbol` string: Binding affinity symbol indicating approximate or precise strength of the binding. - `type` 'ΔG' | 'ΔH' | '-TΔS' | 'EC50' | 'IC50' | 'Ka' | 'Kd' | 'Ki', required: Binding affinity measurement given in one of the following types: The concentration constants: IC50: the concentration of ligand that reduces enzyme activity by 50%; EC50: the concentration of compound that generates a half-maximal response; The binding constant: Kd: dissociation constant; Ka: association constant; Ki: enzyme inhibition constant; The thermodynamic parameters: delta G: Gibbs free energy of binding (for association reaction); delta H: change in enthalpy associated with a chemical reaction; delta S: change in entropy associated with a chemical reaction. - `unit` string, required: Binding affinity unit. Dissociation constant Kd is normally in molar units (or millimolar , micromolar, nanomolar, etc). Association constant Ka is normally expressed in inverse molar units (e.g. M-1). - `value` number, double, required: Binding affinity value between a ligand and its target molecule. - `rcsb_comp_model_provenance` RcsbCompModelProvenance - `entry_id` string, required: Entry identifier corresponding to the computed structure model. - `source_db` 'AlphaFoldDB' | 'ModelArchive': Source database for the computed structure model. - `source_filename` string: Source filename for the computed structure model. - `source_pae_url` string: Source URL for computed structure model predicted aligned error (PAE) json file. - `source_url` string: Source URL for computed structure model file. - `rcsb_entry_container_identifiers` RcsbEntryContainerIdentifiers, required - `assembly_ids` string[]: List of identifiers for assemblies generated from the entry. - `branched_entity_ids` string[]: List of identifiers for the branched entity constituents for the entry. - `emdb_ids` string[]: List of EMDB identifiers for the 3D electron microscopy density maps used in the production of the structure model. - `entity_ids` string[]: List of identifiers or the entity constituents for the entry. - `entry_id` string, required: Entry identifier for the container. - `model_ids` integer[]: List of PDB model identifiers for the entry. - `non_polymer_entity_ids` string[]: List of identifiers for the non-polymer entity constituents for the entry. - `polymer_entity_ids` string[]: List of identifiers for the polymer entity constituents for the entry. - `pubmed_id` integer: Unique integer value assigned to each PubMed record. - `rcsb_id` string: A unique identifier for each object in this entry container. - `related_emdb_ids` string[]: List of EMDB identifiers for the 3D electron microscopy density maps related to the structure model. - `water_entity_ids` string[]: List of identifiers for the solvent/water entity constituents for the entry. - `rcsb_entry_group_membership` RcsbEntryGroupMembership[] - `aggregation_method` 'matching_deposit_group_id', required: Method used to establish group membership - `group_id` string, required: A unique identifier for a group of entries - `rcsb_entry_info` RcsbEntryInfo, required - `assembly_count` integer: The number of assemblies defined for this entry including the deposited assembly. - `branched_entity_count` integer: The number of distinct branched entities in the structure entry. - `branched_molecular_weight_maximum` number, double: The maximum molecular mass (KDa) of a branched entity in the deposited structure entry. - `branched_molecular_weight_minimum` number, double: The minimum molecular mass (KDa) of a branched entity in the deposited structure entry. - `cis_peptide_count` integer: The number of cis-peptide linkages per deposited structure model. - `deposited_atom_count` integer: The number of heavy atom coordinates records (including alternate conformations) for the representative structure model deposited. - `deposited_branched_entity_instance_count` integer: The number of branched instances in the deposited data set. This is the total count of branched entity instances reported per deposited structure model. - `deposited_deuterated_water_count` integer: The number of deuterated water molecules per deposited structure model. - `deposited_hydrogen_atom_count` integer: The number of hydrogen atom coordinates records per deposited structure model. - `deposited_model_count` integer: The number of model structures deposited. - `deposited_modeled_polymer_monomer_count` integer: The number of modeled polymer monomers in the deposited coordinate data. This is the total count of monomers with reported coordinate data for all polymer entity instances in the deposited coordinate data. - `deposited_nonpolymer_entity_instance_count` integer: The number of non-polymer instances in the deposited data set. This is the total count of non-polymer entity instances reported per deposited structure model. - `deposited_polymer_entity_instance_count` integer: The number of protein/nucleic acid polymer instances in the deposited data set. This is the total count of polymer entity instances reported per deposited structure model. - `deposited_polymer_monomer_count` integer: The number of polymer monomers in sample entity instances in the deposited data set. This is the total count of monomers for all polymer entity instances reported per deposited structure model. - `deposited_solvent_atom_count` integer: The number of heavy solvent atom coordinates records per deposited structure model. - `deposited_unmodeled_polymer_monomer_count` integer: The number of unmodeled polymer monomers in the deposited coordinate data. This is the total count of monomers with unreported coordinate data for all polymer entity instances per deposited structure model. - `diffrn_radiation_wavelength_maximum` number, double: The maximum radiation wavelength in angstroms. - `diffrn_radiation_wavelength_minimum` number, double: The minimum radiation wavelength in angstroms. - `disulfide_bond_count` integer: The number of disulfide bonds per deposited structure model. - `entity_count` integer: The number of distinct polymer, non-polymer, branched molecular, and solvent entities per deposited structure model. - `experimental_method` 'EM' | 'Integrative' | 'Multiple methods' | 'NMR' | 'Neutron' | 'Other' | 'X-ray': The category of experimental method(s) used to determine the structure entry. - `experimental_method_count` integer: The number of experimental methods contributing data to the structure determination. - `ihm_multi_scale_flag` 'N' | 'Y': Multi-scale modeling flag for integrative structures. - `ihm_multi_state_flag` 'N' | 'Y': Multi-state modeling flag for integrative structures. - `ihm_ordered_state_flag` 'N' | 'Y': Ordered-state modeling flag for integrative structures. - `ihm_structure_description` string: Description of the integrative structure. - `inter_mol_covalent_bond_count` integer: The number of intermolecular covalent bonds. - `inter_mol_metalic_bond_count` integer: The number of intermolecular metalic bonds. - `molecular_weight` number, double: The molecular mass (KDa) of polymer and non-polymer entities (exclusive of solvent) in the deposited structure entry. - `na_polymer_entity_types` 'DNA (only)' | 'DNA/RNA (only)' | 'NA-hybrid (only)' | 'Other' | 'RNA (only)': Nucleic acid polymer entity type categories describing the entry. - `ndb_struct_conf_na_feature_combined` string[]: This data item identifies secondary structure features of nucleic acids in the entry. - `nonpolymer_bound_components` string[]: Bound nonpolymer components in this entry. - `nonpolymer_entity_count` integer: The number of distinct non-polymer entities in the structure entry exclusive of solvent. - `nonpolymer_molecular_weight_maximum` number, double: The maximum molecular mass (KDa) of a non-polymer entity in the deposited structure entry. - `nonpolymer_molecular_weight_minimum` number, double: The minimum molecular mass (KDa) of a non-polymer entity in the deposited structure entry. - `polymer_composition` 'DNA' | 'DNA/RNA' | 'NA-hybrid' | 'NA/oligosaccharide' | 'RNA' | 'heteromeric protein' | 'homomeric protein' | 'oligosaccharide' | 'other' | 'other type composition' | 'other type pair' | 'protein/NA' | 'protein/NA/oligosaccharide' | 'protein/oligosaccharide': Categories describing the polymer entity composition for the entry. - `polymer_entity_count` integer: The number of distinct polymer entities in the structure entry. - `polymer_entity_count_DNA` integer: The number of distinct DNA polymer entities. - `polymer_entity_count_RNA` integer: The number of distinct RNA polymer entities. - `polymer_entity_count_nucleic_acid` integer: The number of distinct nucleic acid polymer entities (DNA or RNA). - `polymer_entity_count_nucleic_acid_hybrid` integer: The number of distinct hybrid nucleic acid polymer entities. - `polymer_entity_count_protein` integer: The number of distinct protein polymer entities. - `polymer_entity_taxonomy_count` integer: The number of distinct taxonomies represented among the polymer entities in the entry. - `polymer_molecular_weight_maximum` number, double: The maximum molecular mass (KDa) of a polymer entity in the deposited structure entry. - `polymer_molecular_weight_minimum` number, double: The minimum molecular mass (KDa) of a polymer entity in the deposited structure entry. - `polymer_monomer_count_maximum` integer: The maximum monomer count of a polymer entity per deposited structure model. - `polymer_monomer_count_minimum` integer: The minimum monomer count of a polymer entity per deposited structure model. - `representative_model` integer: The chosen representative model. - `resolution_combined` number[]: Combined estimates of experimental resolution contributing to the refined structural model. Resolution reported in "refine.ls_d_res_high" is used for X-RAY DIFFRACTION, FIBER DIFFRACTION, POWDER DIFFRACTION, ELECTRON CRYSTALLOGRAPHY, and NEUTRON DIFFRACTION as identified in "refine.pdbx_refine_id". Resolution reported in "em_3d_reconstruction.resolution" is used for ELECTRON MICROSCOPY. The best value corresponding to "em_3d_reconstruction.resolution_method" == "FSC 0.143 CUT-OFF" is used, if available. If not, the best "em_3d_reconstruction.resolution" value is used. For structures that are not obtained from diffraction-based methods, the resolution values in "refine.ls_d_res_high" are ignored. Multiple values are reported only if multiple methods are used in the structure determination. - `selected_polymer_entity_types` 'Nucleic acid (only)' | 'Oligosaccharide (only)' | 'Other' | 'Protein (only)' | 'Protein/NA' | 'Protein/Oligosaccharide': Selected polymer entity type categories describing the entry. - `software_programs_combined` string[]: Combined list of software programs names reported in connection with the production of this entry. - `solvent_entity_count` integer: The number of distinct solvent entities per deposited structure model. - `structure_determination_methodology` 'computational' | 'experimental' | 'integrative', required: Indicates if the structure was determined using experimental or computational methods. - `structure_determination_methodology_priority` integer: Indicates the priority of the value in _rcsb_entry_info.structure_determination_methodology. The lower the number the higher the priority. Priority values for "experimental" structures is currently set to 10 and the values for "computational" structures is set to 100. - `diffrn_resolution_high` RcsbEntryInfoDiffrnResolutionHigh - `provenance_source` 'Depositor assigned' | 'From refinement resolution cutoff' | 'From the high resolution shell': The provenence source for the high resolution limit of data collection. - `value` number, double: The high resolution limit of data collection. - `rcsb_external_references` RcsbExternalReferences[] - `id` string, required: ID (accession) from external resource linked to this entry. - `link` string: Link to this entry in external resource - `type` 'BMRB' | 'EM DATA RESOURCE' | 'NAKB' | 'NDB' | 'OLDERADO' | 'PROTEIN DIFFRACTION' | 'SB GRID', required: Internal identifier for external resources - `rcsb_ihm_dataset_list` RcsbIhmDatasetList[] - `count` integer: Number of input datasets used in integrative modeling. - `name` '2DEM class average' | '3DEM volume' | 'CX-MS data' | 'Comparative model' | 'Crosslinking-MS data' | 'DNA footprinting data' | 'De Novo model' | 'EM raw micrographs' | 'EPR data' | 'Ensemble FRET data' | 'Experimental model' | 'H/D exchange data' | 'Hydroxyl radical footprinting data' | 'Integrative model' | 'Mass Spectrometry data' | 'Mutagenesis data' | 'NMR data' | 'Other' | 'Predicted contacts' | 'Quantitative measurements of genetic interactions' | 'SAS data' | 'Single molecule FRET data' | 'X-ray diffraction data' | 'Yeast two-hybrid screening data', required: Name of input dataset used in integrative modeling. - `type` 'Computed restraints' | 'Experimental data' | 'Other' | 'Starting model': Type of input dataset used in integrative modeling. - `rcsb_ihm_dataset_source_db_reference` RcsbIhmDatasetSourceDbReference[] - `accession_code` string, required: Accession code for the input dataset. - `db_name` 'AlphaFoldDB' | 'BMRB' | 'BMRbig' | 'BioGRID' | 'EMDB' | 'EMPIAR' | 'MASSIVE' | 'ModelArchive' | 'Other' | 'PDB' | 'PDB-Dev' | 'PRIDE' | 'ProXL' | 'ProteomeXchange' | 'SASBDB' | 'iProX' | 'jPOSTrepo', required: Name of the source database for the input dataset. - `rcsb_ma_qa_metric_global` RcsbMaQaMetricGlobal[] - `model_id` integer, required: The model identifier. - `ma_qa_metric_global` RcsbMaQaMetricGlobalMaQaMetricGlobal[] - `description` string: Description of the global QA metric. - `name` string, required: Name of the global QA metric. - `type` 'PAE' | 'contact probability' | 'distance' | 'energy' | 'ipTM' | 'normalized score' | 'other' | 'pLDDT' | 'pLDDT all-atom' | 'pLDDT all-atom in [0,1]' | 'pLDDT in [0,1]' | 'pTM' | 'zscore', required: The type of global QA metric. - `type_other_details` string: Details for other type of global QA metric. - `value` number, double, required: Value of the global QA metric. - `rcsb_primary_citation` RcsbPrimaryCitation - `book_id_ISBN` string: The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters. - `book_publisher` string: The name of the publisher of the citation; relevant for books or book chapters. - `book_publisher_city` string: The location of the publisher of the citation; relevant for books or book chapters. - `book_title` string: The title of the book in which the citation appeared; relevant for books or book chapters. - `coordinate_linkage` 'n' | 'no' | 'y' | 'yes': _rcsb_primary_citation.coordinate_linkage states whether this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to the creation of the data block, the value of this data item would be 'no'. - `country` string: The country/region of publication; relevant for books and book chapters. - `id` string, required: The value of _rcsb_primary_citation.id must uniquely identify a record in the CITATION list. The _rcsb_primary_citation.id 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. - `journal_abbrev` string: Abbreviated name of the cited journal as given in the Chemical Abstracts Service Source Index. - `journal_id_ASTM` string: The American Society for Testing and Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. - `journal_id_CSD` string: The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Protein Data Bank (PDB). - `journal_id_ISSN` string: The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. - `journal_issue` string: Issue number of the journal cited; relevant for journal articles. - `journal_volume` string: Volume number of the journal cited; relevant for journal articles. - `language` string: Language in which the cited article is written. - `page_first` string: The first page of the citation; relevant for journal articles, books and book chapters. - `page_last` string: The last page of the citation; relevant for journal articles, books and book chapters. - `pdbx_database_id_DOI` string: Document Object Identifier used by doi.org to uniquely specify bibliographic entry. - `pdbx_database_id_PubMed` integer: Ascession number used by PubMed to categorize a specific bibliographic entry. - `rcsb_ORCID_identifiers` string[]: The Open Researcher and Contributor ID (ORCID) identifiers for the citation authors. - `rcsb_authors` string[]: Names of the authors of the citation; relevant for journal articles, books and book chapters. Names are separated by vertical bars. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). - `rcsb_journal_abbrev` string: Normalized journal abbreviation. - `title` string: The title of the citation; relevant for journal articles, books and book chapters. - `year` integer: The year of the citation; relevant for journal articles, books and book chapters. - `refine` Refine[] - `B_iso_max` number, double: The maximum isotropic displacement parameter (B value) found in the coordinate set. - `B_iso_mean` number, double: The mean isotropic displacement parameter (B value) for the coordinate set. - `B_iso_min` number, double: The minimum isotropic displacement parameter (B value) found in the coordinate set. - `aniso_B_1_1` number, double: The [1][1] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. - `aniso_B_1_2` number, double: The [1][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. - `aniso_B_1_3` number, double: The [1][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. - `aniso_B_2_2` number, double: The [2][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. - `aniso_B_2_3` number, double: The [2][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. - `aniso_B_3_3` number, double: The [3][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. - `correlation_coeff_Fo_to_Fc` number, double: The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - ) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections included in the refinement - `correlation_coeff_Fo_to_Fc_free` number, double: The correlation coefficient between the observed and calculated structure factors for reflections not included in the refinement (free reflections). The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - ) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections not included in the refinement (free reflections) - `details` string: Description of special aspects of the refinement process. - `ls_R_factor_R_free` number, double: Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections - `ls_R_factor_R_free_error` number, double: The estimated error in _refine.ls_R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details. - `ls_R_factor_R_free_error_details` string: Special aspects of the method used to estimated the error in _refine.ls_R_factor_R_free. - `ls_R_factor_R_work` number, double: Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections - `ls_R_factor_all` number, double: Residual factor R for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections - `ls_R_factor_obs` number, double: Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections - `ls_d_res_high` number, double: The smallest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the highest resolution. - `ls_d_res_low` number, double: The largest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the lowest resolution. - `ls_matrix_type` 'atomblock' | 'diagonal' | 'full' | 'fullcycle' | 'sparse' | 'userblock': Type of matrix used to accumulate the least-squares derivatives. - `ls_number_parameters` integer: The number of parameters refined in the least-squares process. If possible, this number should include some contribution from the restrained parameters. The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least-squares restraints often depend on geometry or energy considerations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess. - `ls_number_reflns_R_free` integer: The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. - `ls_number_reflns_R_work` integer: The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. - `ls_number_reflns_all` integer: The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. - `ls_number_reflns_obs` integer: The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. - `ls_number_restraints` integer: The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Restrained parameters often involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site.refinement_flags. A general description of refinement constraints may appear in _refine.details. - `ls_percent_reflns_R_free` number, double: The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. - `ls_percent_reflns_obs` number, double: The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. - `ls_redundancy_reflns_all` number, double: The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low to the number of crystallographically unique reflections that satisfy the same limits. - `ls_redundancy_reflns_obs` number, double: The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits. - `ls_wR_factor_R_free` number, double: Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections - `ls_wR_factor_R_work` number, double: Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections - `occupancy_max` number, double: The maximum value for occupancy found in the coordinate set. - `occupancy_min` number, double: The minimum value for occupancy found in the coordinate set. - `overall_FOM_free_R_set` number, double: Average figure of merit of phases of reflections not included in the refinement. This value is derived from the likelihood function. FOM = I~1~(X)/I~0~(X) I~0~, I~1~ = zero- and first-order modified Bessel functions of the first kind X = sigma~A~ |E~o~| |E~c~|/SIGMA E~o~, E~c~ = normalized observed and calculated structure factors sigma~A~ = SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = form factor of atoms delta~x~ = expected error SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = uncertainties of normalized observed structure factors epsilon = multiplicity of the diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. - `overall_FOM_work_R_set` number, double: Average figure of merit of phases of reflections included in the refinement. This value is derived from the likelihood function. FOM = I~1~(X)/I~0~(X) I~0~, I~1~ = zero- and first-order modified Bessel functions of the first kind X = sigma~A~ |E~o~| |E~c~|/SIGMA E~o~, E~c~ = normalized observed and calculated structure factors sigma~A~ = SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = form factor of atoms delta~x~ = expected error SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = uncertainties of normalized observed structure factors epsilon = multiplicity of the diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. - `overall_SU_B` number, double: The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on a maximum-likelihood residual. The overall standard uncertainty (sigma~B~)^2^ gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N~a~ (sigma~B~)^2^ = 8 ---------------------------------------------- sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^4^} N~a~ = number of atoms E~o~ = normalized structure factors m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector SUM_AS = (sigma~A~)^2^/Sigma^2^ Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = experimental uncertainties of normalized structure factors sigma~A~ = SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = atom form factor delta~x~ = expected error epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma~A~ estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU B estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html - `overall_SU_ML` number, double: The overall standard uncertainty (estimated standard deviation) of the positional parameters based on a maximum likelihood residual. The overall standard uncertainty (sigma~X~)^2^ gives an idea of the uncertainty in the position of averagely defined atoms (atoms with B values equal to average B value) 3 N~a~ (sigma~X~)^2^ = --------------------------------------------------------- 8 pi^2^ sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^2^} N~a~ = number of atoms E~o~ = normalized structure factors m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector SUM_AS = (sigma~A~)^2^/Sigma^2^ Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = experimental uncertainties of normalized structure factors sigma~A~ = SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = atom form factor delta~x~ = expected error epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html - `overall_SU_R_Cruickshank_DPI` number, double: The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). The overall standard uncertainty (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N~a~ (sigma~B~)^2^ = 0.65 ---------- (R~value~)^2^ (D~min~)^2^ C^-2/3^ (N~o~-N~p~) N~a~ = number of atoms included in refinement N~o~ = number of observations N~p~ = number of parameters refined R~value~ = conventional crystallographic R value D~min~ = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html - `overall_SU_R_free` number, double: The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the free R value. The overall standard uncertainty (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N~a~ (sigma~B~)^2^ = 0.65 ---------- (R~free~)^2^ (D~min~)^2^ C^-2/3^ (N~o~-N~p~) N~a~ = number of atoms included in refinement N~o~ = number of observations N~p~ = number of parameters refined R~free~ = conventional free crystallographic R value calculated using reflections not included in refinement D~min~ = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html - `pdbx_R_Free_selection_details` string: Details of the manner in which the cross validation reflections were selected. - `pdbx_TLS_residual_ADP_flag` 'LIKELY RESIDUAL' | 'UNVERIFIED': A flag for TLS refinements identifying the type of atomic displacement parameters stored in _atom_site.B_iso_or_equiv. - `pdbx_average_fsc_free` number, double: Average Fourier Shell Correlation (avgFSC) between model and observed structure factors for reflections not included in refinement. The average FSC is a measure of the agreement between observed and calculated structure factors. sum(N~i~ FSC~free-i~) avgFSC~free~ = --------------------- sum(N~i~) N~i~ = the number of free reflections in the resolution shell i FSC~free-i~ = FSC for free reflections in the i-th resolution shell calculated as: (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~free-i~ = ------------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation of FSC~free-i~ is carried over all free reflections in the resolution shell. Summation of avgFSC~free~ is carried over all resolution shells. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). - `pdbx_average_fsc_overall` number, double: Overall average Fourier Shell Correlation (avgFSC) between model and observed structure factors for all reflections. The average FSC is a measure of the agreement between observed and calculated structure factors. sum(N~i~ FSC~i~) avgFSC = ---------------- sum(N~i~) N~i~ = the number of all reflections in the resolution shell i FSC~i~ = FSC for all reflections in the i-th resolution shell calculated as: (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~i~ = ------------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation of FSC~i~ is carried over all reflections in the resolution shell. Summation of avgFSC is carried over all resolution shells. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). - `pdbx_average_fsc_work` number, double: Average Fourier Shell Correlation (avgFSC) between model and observed structure factors for reflections included in refinement. The average FSC is a measure of the agreement between observed and calculated structure factors. sum(N~i~ FSC~work-i~) avgFSC~work~ = --------------------- sum(N~i~) N~i~ = the number of working reflections in the resolution shell i FSC~work-i~ = FSC for working reflections in the i-th resolution shell calculated as: (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~work-i~ = ------------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation of FSC~work-i~ is carried over all working reflections in the resolution shell. Summation of avgFSC~work~ is carried over all resolution shells. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). - `pdbx_data_cutoff_high_absF` number, double: Value of F at "high end" of data cutoff. - `pdbx_data_cutoff_high_rms_absF` number, double: Value of RMS |F| used as high data cutoff. - `pdbx_data_cutoff_low_absF` number, double: Value of F at "low end" of data cutoff. - `pdbx_diffrn_id` string[]: An identifier for the diffraction data set used in this refinement. Multiple diffraction data sets specified as a comma separated list. - `pdbx_isotropic_thermal_model` string: Whether the structure was refined with indvidual isotropic, anisotropic or overall temperature factor. - `pdbx_ls_cross_valid_method` string: Whether the cross validataion method was used through out or only at the end. - `pdbx_ls_sigma_F` number, double: Data cutoff (SIGMA(F)) - `pdbx_ls_sigma_Fsqd` number, double: Data cutoff (SIGMA(F^2)) - `pdbx_ls_sigma_I` number, double: Data cutoff (SIGMA(I)) - `pdbx_method_to_determine_struct` string: Method(s) used to determine the structure. - `pdbx_overall_ESU_R` number, double: Overall estimated standard uncertainties of positional parameters based on R value. - `pdbx_overall_ESU_R_Free` number, double: Overall estimated standard uncertainties of positional parameters based on R free value. - `pdbx_overall_SU_R_Blow_DPI` number, double: The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). Ref: Blow, D (2002) Acta Cryst. D58, 792-797 - `pdbx_overall_SU_R_free_Blow_DPI` number, double: The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R-free value, expressed in a formalism known as the dispersion precision indicator (DPI). Ref: Blow, D (2002) Acta Cryst. D58, 792-797 - `pdbx_overall_SU_R_free_Cruickshank_DPI` number, double: The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R-free value, expressed in a formalism known as the dispersion precision indicator (DPI). Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. - `pdbx_overall_phase_error` number, double: The overall phase error for all reflections after refinement using the current refinement target. - `pdbx_refine_id` string, required: This data item uniquely identifies a refinement within an entry. _refine.pdbx_refine_id can be used to distinguish the results of joint refinements. - `pdbx_solvent_ion_probe_radii` number, double: For bulk solvent mask calculation, the amount that the ionic radii of atoms, which can be ions, are increased used. - `pdbx_solvent_shrinkage_radii` number, double: For bulk solvent mask calculation, amount mask is shrunk after taking away atoms with new radii and a constant value assigned to this new region. - `pdbx_solvent_vdw_probe_radii` number, double: For bulk solvent mask calculation, the value by which the vdw radii of non-ion atoms (like carbon) are increased and used. - `pdbx_starting_model` string: Starting model for refinement. Starting model for molecular replacement should refer to a previous structure or experiment. - `pdbx_stereochem_target_val_spec_case` string: Special case of stereochemistry target values used in SHELXL refinement. - `pdbx_stereochemistry_target_values` string: Stereochemistry target values used in refinement. - `solvent_model_details` string: Special aspects of the solvent model used during refinement. - `solvent_model_param_bsol` number, double: The value of the BSOL solvent-model parameter describing the average isotropic displacement parameter of disordered solvent atoms. This is one of the two parameters (the other is _refine.solvent_model_param_ksol) in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268. - `solvent_model_param_ksol` number, double: The value of the KSOL solvent-model parameter describing the ratio of the electron density in the bulk solvent to the electron density in the molecular solute. This is one of the two parameters (the other is _refine.solvent_model_param_bsol) in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268. - `refine_analyze` RefineAnalyze[] - `Luzzati_coordinate_error_free` number, double: The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. - `Luzzati_coordinate_error_obs` number, double: The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. - `Luzzati_d_res_low_free` number, double: The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. - `Luzzati_d_res_low_obs` number, double: The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. - `Luzzati_sigma_a_free` number, double: The value of sigma~a~ used in constructing the Luzzati plot for the reflections treated as a test set during refinement. Details of the estimation of sigma~a~ can be specified in _refine_analyze.Luzzati_sigma_a_free_details. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. - `Luzzati_sigma_a_obs` number, double: The value of sigma~a~ used in constructing the Luzzati plot for reflections classified as observed. Details of the estimation of sigma~a~ can be specified in _refine_analyze.Luzzati_sigma_a_obs_details. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. - `number_disordered_residues` number, double: The number of discretely disordered residues in the refined model. - `occupancy_sum_hydrogen` number, double: The sum of the occupancies of the hydrogen atoms in the refined model. - `occupancy_sum_non_hydrogen` number, double: The sum of the occupancies of the non-hydrogen atoms in the refined model. - `pdbx_Luzzati_d_res_high_obs` number, double: record the high resolution for calculating Luzzati statistics. - `pdbx_refine_id` string, required: This data item uniquely identifies a refinement within an entry. _refine_analyze.pdbx_refine_id can be used to distinguish the results of joint refinements. - `refine_hist` RefineHist[] - `cycle_id` string, required: The value of _refine_hist.cycle_id must uniquely identify a record in the REFINE_HIST list. Note that this item need not be a number; it can be any unique identifier. - `d_res_high` number, double: The lowest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the highest resolution. - `d_res_low` number, double: The highest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the lowest resolution. - `number_atoms_solvent` integer: The number of solvent atoms that were included in the model at this cycle of the refinement. - `number_atoms_total` integer: The total number of atoms that were included in the model at this cycle of the refinement. - `pdbx_B_iso_mean_ligand` number, double: Mean isotropic B-value for ligand molecules included in refinement. - `pdbx_B_iso_mean_solvent` number, double: Mean isotropic B-value for solvent molecules included in refinement. - `pdbx_number_atoms_ligand` integer: Number of ligand atoms included in refinement - `pdbx_number_atoms_nucleic_acid` integer: Number of nucleic atoms included in refinement - `pdbx_number_atoms_protein` integer: Number of protein atoms included in refinement - `pdbx_number_residues_total` integer: Total number of polymer residues included in refinement. - `pdbx_refine_id` string, required: This data item uniquely identifies a refinement within an entry. _refine_hist.pdbx_refine_id can be used to distinguish the results of joint refinements. - `refine_ls_restr` RefineLsRestr[] - `dev_ideal` number, double: For the given parameter type, the root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. For instance, bond distances may deviate by 0.018 \%A (r.m.s.) from ideal values in the current model. - `dev_ideal_target` number, double: For the given parameter type, the target root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. - `number` integer: The number of parameters of this type subjected to restraint in least-squares refinement. - `pdbx_refine_id` string, required: This data item uniquely identifies a refinement within an entry. _refine_ls_restr.pdbx_refine_id can be used to distinguish the results of joint refinements. - `pdbx_restraint_function` string: The functional form of the restraint function used in the least-squares refinement. - `type` string, required: The type of the parameter being restrained. Explicit sets of data values are provided for the programs PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with RESTRAIN_). As computer programs change, these data values are given as examples, not as an enumeration list. Computer programs that convert a data block to a refinement table will expect the exact form of the data values given here to be used. - `weight` number, double: The weighting value applied to this type of restraint in the least-squares refinement. - `reflns` Reflns[] - `B_iso_Wilson_estimate` number, double: The value of the overall isotropic displacement parameter estimated from the slope of the Wilson plot. - `R_free_details` string: A description of the method by which a subset of reflections was selected for exclusion from refinement so as to be used in the calculation of a 'free' R factor. - `Rmerge_F_all` number, double: Residual factor Rmerge for all reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection - `Rmerge_F_obs` number, double: Residual factor Rmerge for reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection - `d_resolution_high` number, double: The smallest value in angstroms for the interplanar spacings for the reflection data. This is called the highest resolution. - `d_resolution_low` number, double: The largest value in angstroms for the interplanar spacings for the reflection data. This is called the lowest resolution. - `data_reduction_details` string: A description of special aspects of the data-reduction procedures. - `data_reduction_method` string: The method used for data reduction. Note that this is not the computer program used, which is described in the SOFTWARE category, but the method itself. This data item should be used to describe significant methodological options used within the data-reduction programs. - `details` string: A description of reflection data not covered by other data names. This should include details of the Friedel pairs. - `limit_h_max` integer: Maximum value of the Miller index h for the reflection data. This need not have the same value as _diffrn_reflns.limit_h_max. - `limit_h_min` integer: Minimum value of the Miller index h for the reflection data. This need not have the same value as _diffrn_reflns.limit_h_min. - `limit_k_max` integer: Maximum value of the Miller index k for the reflection data. This need not have the same value as _diffrn_reflns.limit_k_max. - `limit_k_min` integer: Minimum value of the Miller index k for the reflection data. This need not have the same value as _diffrn_reflns.limit_k_min. - `limit_l_max` integer: Maximum value of the Miller index l for the reflection data. This need not have the same value as _diffrn_reflns.limit_l_max. - `limit_l_min` integer: Minimum value of the Miller index l for the reflection data. This need not have the same value as _diffrn_reflns.limit_l_min. - `number_all` integer: The total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. The item _reflns.details describes the reflection data. - `number_obs` integer: The number of reflections in the REFLN list (not the DIFFRN_REFLN list) classified as observed (see _reflns.observed_criterion). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. - `observed_criterion` string: The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold. - `observed_criterion_F_max` number, double: The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of F. - `observed_criterion_F_min` number, double: The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of F. - `observed_criterion_I_max` number, double: The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of I. - `observed_criterion_I_min` number, double: The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of I. - `observed_criterion_sigma_F` number, double: The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(F). - `observed_criterion_sigma_I` number, double: The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(I). - `pdbx_CC_half` number, double: The Pearson's correlation coefficient expressed as a decimal value between the average intensities from randomly selected half-datasets. Ref: Karplus & Diederichs (2012), Science 336, 1030-33 - `pdbx_R_split` number, double: R split measures the agreement between the sets of intensities created by merging odd- and even-numbered images from the overall data. Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341 - `pdbx_Rmerge_I_obs` number, double: The R value for merging intensities satisfying the observed criteria in this data set. - `pdbx_Rpim_I_all` number, double: The precision-indicating merging R factor value Rpim, for merging all intensities in this data set. sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - | Rpim = -------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. - `pdbx_Rrim_I_all` number, double: The redundancy-independent merging R factor value Rrim, also denoted Rmeas, for merging all intensities in this data set. sum~i~ [N~i~/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - | Rrim = ---------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. - `pdbx_Rsym_value` number, double: The R sym value as a decimal number. - `pdbx_chi_squared` number, double: Overall Chi-squared statistic. - `pdbx_diffrn_id` string[]: An identifier for the diffraction data set for this set of summary statistics. Multiple diffraction data sets entered as a comma separated list. - `pdbx_netI_over_av_sigmaI` number, double: The ratio of the average intensity to the average uncertainty, /. - `pdbx_netI_over_sigmaI` number, double: The mean of the ratio of the intensities to their standard uncertainties, . - `pdbx_number_measured_all` integer: Total number of measured reflections. - `pdbx_ordinal` integer, required: An ordinal identifier for this set of reflection statistics. - `pdbx_redundancy` number, double: Overall redundancy for this data set. - `pdbx_scaling_rejects` integer: Number of reflections rejected in scaling operations. - `percent_possible_obs` number, double: The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion. - `phase_calculation_details` string: The value of _reflns.phase_calculation_details describes a special details about calculation of phases in _refln.phase_calc. - `reflns_shell` ReflnsShell[] - `Rmerge_F_all` number, double: Residual factor Rmerge for all reflections that satisfy the resolution limits established by _reflns_shell.d_res_high and _reflns_shell.d_res_low. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection - `Rmerge_F_obs` number, double: Residual factor Rmerge for reflections that satisfy the resolution limits established by _reflns_shell.d_res_high and _reflns_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection - `Rmerge_I_all` number, double: The value of Rmerge(I) for all reflections in a given shell. sum~i~(sum~j~|I~j~ - |) Rmerge(I) = -------------------------- sum~i~(sum~j~) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection - `Rmerge_I_obs` number, double: The value of Rmerge(I) for reflections classified as 'observed' (see _reflns.observed_criterion) in a given shell. sum~i~(sum~j~|I~j~ - |) Rmerge(I) = -------------------------- sum~i~(sum~j~) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection - `d_res_high` number, double: The smallest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the highest resolution. - `d_res_low` number, double: The highest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the lowest resolution. - `meanI_over_sigI_all` number, double: The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. - `meanI_over_sigI_obs` number, double: The ratio of the mean of the intensities of the reflections classified as 'observed' (see _reflns.observed_criterion) in this shell to the mean of the standard uncertainties of the intensities of the 'observed' reflections in this shell. - `meanI_over_uI_all` number, double: The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. - `number_measured_all` integer: The total number of reflections measured for this shell. - `number_measured_obs` integer: The number of reflections classified as 'observed' (see _reflns.observed_criterion) for this shell. - `number_possible` integer: The number of unique reflections it is possible to measure in this shell. - `number_unique_all` integer: The total number of measured reflections which are symmetry- unique after merging for this shell. - `number_unique_obs` integer: The total number of measured reflections classified as 'observed' (see _reflns.observed_criterion) which are symmetry-unique after merging for this shell. - `pdbx_CC_half` number, double: The Pearson's correlation coefficient expressed as a decimal value between the average intensities from randomly selected half-datasets within the resolution shell. Ref: Karplus & Diederichs (2012), Science 336, 1030-33 - `pdbx_R_split` number, double: R split measures the agreement between the sets of intensities created by merging odd- and even-numbered images from the data within the resolution shell. Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341 - `pdbx_Rpim_I_all` number, double: The precision-indicating merging R factor value Rpim, for merging all intensities in a given shell. sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - | Rpim = -------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. - `pdbx_Rrim_I_all` number, double: The redundancy-independent merging R factor value Rrim, also denoted Rmeas, for merging all intensities in a given shell. sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - | Rrim = -------------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. - `pdbx_Rsym_value` number, double: R sym value in percent. - `pdbx_chi_squared` number, double: Chi-squared statistic for this resolution shell. - `pdbx_diffrn_id` string[]: An identifier for the diffraction data set corresponding to this resolution shell. Multiple diffraction data sets specified as a comma separated list. - `pdbx_netI_over_sigmaI_all` number, double: The mean of the ratio of the intensities to their standard uncertainties of all reflections in the resolution shell. _reflns_shell.pdbx_netI_over_sigmaI_all = - `pdbx_netI_over_sigmaI_obs` number, double: The mean of the ratio of the intensities to their standard uncertainties of observed reflections (see _reflns.observed_criterion) in the resolution shell. _reflns_shell.pdbx_netI_over_sigmaI_obs = - `pdbx_ordinal` integer, required: An ordinal identifier for this resolution shell. - `pdbx_redundancy` number, double: Redundancy for the current shell. - `pdbx_rejects` integer: The number of rejected reflections in the resolution shell. Reflections may be rejected from scaling by setting the observation criterion, _reflns.observed_criterion. - `percent_possible_all` number, double: The percentage of geometrically possible reflections represented by all reflections measured for this shell. - `percent_possible_obs` number, double: The percentage of geometrically possible reflections represented by reflections classified as 'observed' (see _reflns.observed_criterion) for this shell. - `software` Software[] - `citation_id` string: This data item is a pointer to _citation.id in the CITATION category. - `classification` string: The classification of the program according to its major function. - `contact_author` string: The recognized contact author of the software. This could be the original author, someone who has modified the code or someone who maintains the code. It should be the person most commonly associated with the code. - `contact_author_email` string: The e-mail address of the person specified in _software.contact_author. - `date` string: The date the software was released. - `description` string: Description of the software. - `language` 'Ada' | 'Awk' | 'Basic' | 'C' | 'C++' | 'C/C++' | 'Fortran' | 'Fortran 77' | 'Fortran 90' | 'Fortran_77' | 'Java' | 'Java & Fortran' | 'Other' | 'Pascal' | 'Perl' | 'Python' | 'Python/C++' | 'Tcl' | 'assembler' | 'csh' | 'ksh' | 'sh': The major computing language in which the software is coded. - `location` string: The URL for an Internet address at which details of the software can be found. - `name` string: The name of the software. - `os` string: The name of the operating system under which the software runs. - `pdbx_ordinal` integer, required: An ordinal index for this category - `type` 'filter' | 'jiffy' | 'library' | 'other' | 'package' | 'program': The classification of the software according to the most common types. - `version` string: The version of the software. - `struct` Struct - `pdbx_CASP_flag` 'N' | 'Y': The item indicates whether the entry is a CASP target, a CASD-NMR target, or similar target participating in methods development experiments. - `pdbx_descriptor` string: An automatically generated descriptor for an NDB structure or the unstructured content of the PDB COMPND record. - `pdbx_model_details` string: Text description of the methodology which produced this model structure. - `pdbx_model_type_details` string: A description of the type of structure model. - `title` string: A title for the data block. The author should attempt to convey the essence of the structure archived in the CIF in the title, and to distinguish this structural result from others. - `struct_keywords` StructKeywords - `pdbx_keywords` string: Terms characterizing the macromolecular structure. - `text` string: Keywords describing this structure. - `symmetry` Symmetry - `Int_Tables_number` integer: Space-group number from International Tables for Crystallography Vol. A (2002). - `cell_setting` 'cubic' | 'hexagonal' | 'monoclinic' | 'orthorhombic' | 'rhombohedral' | 'tetragonal' | 'triclinic' | 'trigonal': The cell settings for this space-group symmetry. - `pdbx_full_space_group_name_H_M` string: Used for PDB space group: Example: 'C 1 2 1' (instead of C 2) 'P 1 2 1' (instead of P 2) 'P 1 21 1' (instead of P 21) 'P 1 1 21' (instead of P 21 -unique C axis) 'H 3' (instead of R 3 -hexagonal) 'H 3 2' (instead of R 3 2 -hexagonal) - `space_group_name_H_M` string: Hermann-Mauguin space-group symbol. Note that the Hermann-Mauguin symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used, always supply the FULL symbol from International Tables for Crystallography Vol. A (2002) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol, specify the _symmetry_equiv.pos_as_xyz or _symmetry.space_group_name_Hall data items as well. Leave spaces between symbols referring to different axes. - `space_group_name_Hall` string: Space-group symbol as described by Hall (1981). This symbol gives the space-group setting explicitly. Leave spaces between the separate components of the symbol. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981) A37, 921. - `rcsb_id` string, required: A unique identifier for each object in this entry container. ## Other responses - `404`: Not Found --- [API](https://skmtc.dev/rcsb/apis/rcsb-pdb-data-api.md) - [All operations](https://skmtc.dev/rcsb/apis/rcsb-pdb-data-api/llms.txt) - [OpenAPI document](https://skmtc.dev/rcsb/apis/rcsb-pdb-data-api/revisions/60c1f3a4b5b1?raw)