DATA ITEMS RECOMMENDED FOR DEPOSITING CRYSTALLOGRAPHIC STRUCTURE DETERMINATIONS

DATA ITEMS RECOMMENDED FOR DEPOSITING NMR STRUCTURE DETERMINATIONS

(Revised: 05-Oct-2002)

Please email jwest@rcsb.rutgers.edu with any comments/questions on these items.

Further details are available from http://mmcif.rcsb.org

(Status items: PDB=Currently in PDB mmCIF=defined in PDB exchange data dictionary)

MOLECULAR INFORMATION:

Data Item	Dictionary Item Name	Status	Comments
Macromolecules
Molecule name	_entity.pdbx_description holds the name corresponding to PDB compound name. Multiple systematic and common names can be supplied in mmCIF categories entity_name_sys and entity_name_com	PDB,mmCIF
Sequence (one-letter code)	_entity_poly.pdbx_seq_one_letter_code	PDB,mmCIF
Fragment	_entity.pdbx_fragment	PDB,mmCIF
Mutations	_entity.pdbx_mutation	PDB,mmCIF
Modifications (e.g. chemical or post-translational modifications)	_entity.pdbx_modification	mmCIF
Experimental Mass	_entity.pdbx_formula_weight_exptl _entity.pdbx_formula_weight_exptl_meth	mmCIF
E.C. number	_entity.pdbx_ec	PDB,mmCIF
Non-polymers
Molecule name	_chem_comp.name	PDB,mmCIF
Molecular topology	mmCIF categories chem_comp_atom and chem_comp_bond for any non-polymer molecules not describe in the PDB ligand dictionary.	PDB,mmCIF

Notes: Macromolecule names are recorded in PDB COMPND records. All of the above items are included in the current format. The assignment of multiple common and systematic names is supported by mmCIF but not in the PDB format.

SOURCE INFORMATION:

Data Item	Dictionary Item Name	Status	Comments
Organism common name	_entity_src_gen.gene_src_common_name	PDB,mmCIF
Organism scientific name	_entity_src_gen.pdbx_gene_src_scientific_name	PDB,mmCIF
Organ	_entity_src_gen.pdbx_gene_src_organ	PDB,mmCIF
Gene	_entity_src_gen.pdbx_gene_src_gene	PDB,mmCIF
Cellular location	_entity_src_gen.pdbx_gene_src_cellular_location	PDB,mmCIF

Expression system common name	_entity_src_gen.host_org_common_name	PDB,mmCIF
Expression system scientific name	_entity_src_gen.pdbx_host_org_scientific_name	PDB,mmCIF
Expression system cell line	_entity_src_gen.pdbx_host_org_cell_line	PDB,mmCIF
Expression system strain	_entity_src_gen.pdbx_host_org_strain	PDB,mmCIF
Expression system variant	_entity_src_gen.pdbx_host_org_variant	PDB,mmCIF
Expression vector	_entity_src_gen.pdbx_host_org_vector	PDB,mmCIF
Expression plasmid	_entity_src_gen.plasmid_name	PDB,mmCIF
Expression system cellular location	_entity_src_gen.pdbx_host_org_cellular_location	PDB,mmCIF
Expression system gene	_entity_src_gen.pdbx_host_org_gene	PDB,mmCIF

Notes: Source information is recorded in PDB SOURCE records. All of the above source items are represented in the current format. Source information is greatly expanded in the recommendations for deposition of protein production data.

SAMPLE CONDITIONS:

Data Item	Dictionary Item Name	Status	Comments
Solution number	_pdbx_nmr_exptl_sample.solution_id	mmCIF
Molecular component	_pdbx_nmr_exptl_sample.component	mmCIF
Concentration	_pdbx_nmr_exptl_sample.concentration	mmCIF
Concentration units	_pdbx_nmr_exptl_sample.concentration_units	mmCIF
Isotopic labeling	_pdbx_nmr_exptl_sample.isotopic_labeling	mmCIF

Experimental conditions identifier	_pdbx_nmr_exptl_sample_conditions.conditions_id	mmCIF
Temperature	_pdbx_nmr_exptl_sample_conditions.temperature	mmCIF
Pressure units	_pdbx_nmr_exptl_sample_conditions.pressure_units	mmCIF
Pressure	_pdbx_nmr_exptl_sample_conditions.pressure	mmCIF
pH	_pdbx_nmr_exptl_sample_conditions.pH	mmCIF
Ionic strength	_pdbx_nmr_exptl_sample_conditions.ionic_strength	mmCIF

DATA COLLECTION APPARATUS:

Data Item	Dictionary Item Name	Status	Comments
Spectrometer number	_pdbx_nmr_spectrometer.spectrometer_id	mmCIF
Spectrometer model	_pdbx_nmr_spectrometer.model	mmCIF
Spectrometer type	_pdbx_nmr_spectrometer.type	mmCIF
Spectrometer manufacturer	_pdbx_nmr_spectrometer.manufacturer	mmCIF
Spectrometer field strength	_pdbx_nmr_spectrometer.field_strength	mmCIF
Probe type	_pdbx_nmr_spectrometer.probe_type	mmCIF
Probe diameter	_pdbx_nmr_spectrometer.probe_diameter	mmCIF
Probe manufacturer	_pdbx_nmr_spectrometer.probe_manufacturer	mmCIF

DESCRIPTION OF EXPERIMENTS:

Data Item	Dictionary Item Name	Status	Comments
Experiment number	_pdbx_nmr_exptl.experiment_id	mmCIF
Experimental conditions identifier	_pdbx_nmr_exptl.conditions_id	mmCIF
Solution number	_pdbx_nmr_exptl.solution_id	mmCIF
Experiment type (e.g. 3D_15N-separated NOESY)	_pdbx_nmr_exptl.type	mmCIF

SOFTWARE:

Data Item	Dictionary Item Name	Status	Comments
Software type/classification	_pdbx_nmr_software.classification	mmCIF
Program name	_pdbx_nmr_software.name	mmCIF
Program version	_pdbx_nmr_software.version	mmCIF
Authors	_pdbx_nmr_software.authors	mmCIF

CONSTRAINT STATISTICS:

Data Item	Dictionary Item Name	Status
Total NOEs	_pdbx_nmr_constraints.NOE_constraints_total	mmCIF
Total intraresidue NOEs	_pdbx_nmr_constraints.NOE_intraresidue_total_count	mmCIF
Total inter-entity NOES	_pdbx_nmr_constraints.NOE_interentity_total_count	mmCIF
Total sequential NOEs	_pdbx_nmr_constraints.NOE_sequential_total_count	mmCIF
Total medium-range NOEs	_pdbx_nmr_constraints.NOE_medium_range_total_count	mmCIF
Total long-range NOEs	_pdbx_nmr_constraints.NOE_long_range_total_count	mmCIF
Protein phi-angle constraints	_pdbx_nmr_constraints.protein_phi_angle_constraints_total_count	mmCIF
Protein psi-angle constraints	_pdbx_nmr_constraints.protein_psi_angle_constraints_total_count	mmCIF
Protein chi-angle constraints	_pdbx_nmr_constraints.protein_chi_angle_constraints_total_count	mmCIF
Protein angle constraints (other)	_pdbx_nmr_constraints.protein_other_angle_constraints_total_count	mmCIF
H-bond constraints	_pdbx_nmr_constraints.hydrogen_bond_constraints_total_count	mmCIF
Disulfide bond constraints	_pdbx_nmr_constraints.disulfide_bond_constraints_total_count	mmCIF
Nucleic acid alpha-angle constraints	_pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count	mmCIF
Nucleic acid beta-angle constraints	_pdbx_nmr_constraints.NA_beta-angle_constraints_total_count	mmCIF
Nucleic acid gamma-angle constraints	_pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count	mmCIF
Nucleic acid delta-angle constraints	_pdbx_nmr_constraints.NA_delta-angle_constraints_total_count	mmCIF
Nucleic acid epsilon-angle constraints	_pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count	mmCIF
Nucleic acid chi-angle constraints	_pdbx_nmr_constraints.NA_chi-angle_constraints_total_count	mmCIF
Nucleic acid angle constraints other	_pdbx_nmr_constraints.NA_other-angle_constraints_total_count	mmCIF
Nucleic acid sugar pucker constraints	_pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count	mmCIF
Inter-proton NOE distance evaluation	_pdbx_nmr_constraints.NOE_interproton_distance_evaluation	mmCIF
NOE pseudoatom corrections	_pdbx_nmr_constraints.NOE_pseudoatom_corrections	mmCIF
NOE motional averaging corrections	_pdbx_nmr_constraints.NOE_motional_averaging_correction	mmCIF

ENSEMBLE STATISTICS:

Data Item	Dictionary Item Name	Status
Total calculated conformers	_pdbx_nmr_ensemble.conformers_calculated_total_number	mmCIF
Total submitted conformers	_pdbx_nmr_ensemble.conformers_submitted_total_number	mmCIF
Conformer selection criteria	_pdbx_nmr_ensemble.conformer_selection_criteria	mmCIF
Representative conformer number	_pdbx_nmr_ensemble.representative_conformer	mmCIF
Average constraints per residue	_pdbx_nmr_ensemble.average_constraints_per_residue	mmCIF
Average constraint violations per residue	_pdbx_nmr_ensemble.average_constraint_violations_per_residue	mmCIF
Maximum distance constraint violation	_pdbx_nmr_ensemble.maximum_distance_constraint_violation	mmCIF
Average distance constraint violation	_pdbx_nmr_ensemble.average_distance_constraint_violation	mmCIF
Maximum upper distance constraint violation	_pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation	mmCIF
Maximum lower distance constraint violation	_pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation	mmCIF
Distance constraint violation method	_pdbx_nmr_ensemble.distance_constraint_violation_method	mmCIF
Maximum torsion angle constraint violation	_pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation	mmCIF
Average torsion angle constraint violation	_pdbx_nmr_ensemble.average_torsion_angle_constraint_violation	mmCIF
Torsion angle constraint violation method	_pdbx_nmr_ensemble.torsion_angle_constraint_violation_method	mmCIF

Structure range for RMSD calculation	_pdbx_nmr_ensemble_rms.residue_range_begin _pdbx_nmr_ensemble_rms.chain_range_begin _pdbx_nmr_ensemble_rms.residue_range_end _pdbx_nmr_ensemble_rms.chain_range_end	mmCIF
Atom type filter	_pdbx_nmr_ensemble_rms.atom_type	mmCIF
Overall (RMSD)	_pdbx_nmr_ensemble_rms.distance_rms_dev	mmCIF
Overall (RMSD) error	_pdbx_nmr_ensemble_rms.distance_rms_dev_error	mmCIF
Covalent bonds (RMSD)	_pdbx_nmr_ensemble_rms.covalent_bond_rms_dev	mmCIF
Covalent bonds (RMSD) error	_pdbx_nmr_ensemble_rms.covalent_bond_rms_dev_error	mmCIF
Covalent bond angle (RMSD)	_pdbx_nmr_ensemble_rms.bond_angle_rms_dev	mmCIF
Covalent bond angle (RMSD) error	_pdbx_nmr_ensemble_rms.bond_angle_rms_dev_error	mmCIF
Improper torsion (RMSD)	_pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev	mmCIF
Improper torsion (RMSD) error	_pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error	mmCIF
Peptide planarity (RMSD)	_pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev	mmCIF
Peptide planarity (RMSD) error	_pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev_error	mmCIF
Dihedral angles (RMSD)	_pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev	mmCIF
Dihedral angles (RMSD) error	_pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev_error	mmCIF
Coordinate average/RMSD method	_pdbx_nmr_ensemble_rms.coord_average_rmsd_method	mmCIF

REPRESENTATIVE STRUCTURES:

Data Item	Dictionary Item Name	Status
Representative conformer number	_pdbx_nmr_representative.conformer_id	mmCIF
Conformer selection criteria	_pdbx_nmr_representative.selection_criteria	mmCIF

REFINEMENT DETAILS:

Data Item	Dictionary Item Name	Status
Refinement method	_pdbx_nmr_refine.method	mmCIF
Additional refinement details	_pdbx_nmr_refine.details	mmCIF

FORCE CONSTANTS:

Data Item

Dictionary Item Name

Status

Distance force constant

_pdbx_nmr_force_constants.exptl_distance_term

_pdbx_nmr_force_constants.exptl_distance_term_units

mmCIF

Torsion angle force constant

_pdbx_nmr_force_constants.exptl_torsion_angles_term

_pdbx_nmr_force_constants.exptl_torsion_angles_term_units

mmCIF

J-coupling force constant

_pdbx_nmr_force_constants.exptl_J_coupling_term

_pdbx_nmr_force_constants.exptl_J_coupling_term_units

mmCIF

¹³C force constant

_pdbx_nmr_force_constants.exptl_13C_shift_term

_pdbx_nmr_force_constants.exptl_13C_shift_term_units

mmCIF

¹H shift force constant

_pdbx_nmr_force_constants.exptl_1H_shift_term

_pdbx_nmr_force_constants.exptl_1H_shift_term_units

mmCIF

Dipolar coupling force constant

_pdbx_nmr_force_constants.exptl_dipolar_coupling_term

_pdbx_nmr_force_constants.exptl_dipolar_coupling_term_units

mmCIF

D isotope force constant

_pdbx_nmr_force_constants.exptl_D_isotope_shift_term

_pdbx_nmr_force_constants.exptl_D_isotope_shift_term_units

mmCIF

Covalent bond force constant

_pdbx_nmr_force_constants.covalent_geom_bond_term

_pdbx_nmr_force_constants.covalent_geom_bond_term_units

mmCIF

Covalent bond angle force constant

_pdbx_nmr_force_constants.covalent_geom_angles_term

_pdbx_nmr_force_constants.covalent_geom_angles_term_units

mmCIF

Improper torsion force constant

_pdbx_nmr_force_constants.covalent_geom_impropers_term

_pdbx_nmr_force_constants.covalent_geom_impropers_term_units

mmCIF

Van der Waals force constant

_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type

_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term

_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_units

mmCIF

Non-bonded interactions force constant

_pdbx_nmr_force_constants.non-bonded_inter_conf_db_potential_term

mmCIF

Radius of gyration force constant

_pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term

_pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term_units

mmCIF

MODEL COORDINATES AND RELATED INFORMATION:

Data Item	Dictionary Item Name	Status	Comments
Atomic coordinates for each model or representative conformer	mmCIF category atom_site	PDB,mmCIF
Secondary structure assignments	mmCIF categories struct_conf, struct_conf_type, struct_sheet_*, pdbx_struct_sheet_hbond	PDB,mmCIF
Disulfide bonds, hydrogen bonds, and salt bridges	mmCIF categories struct_conn and struct_conn_type	PDB,mmCIF

ADDITIONAL INFORMATION ABOUT EACH DEPOSITION:

Data Item	Dictionary Item Name	Status	Comments
Author contact information	mmCIF category audit_contact_author	PDB,mmCIF
Release status (e.g. release immediately, hold for 6 months)	_pdbx_database_status.dep_release_code_coordinates _pdbx_database_status.dep_release_code_struct_fact _pdbx_database_status.dep_release_code_sequence	PDB,mmCIF
Citation	mmCIF categories citation and citation_author	PDB,mmCIF
Related database information (e.g. sequence/target database ids)	mmCIF category pdbx_database_related	PDB,mmCIF


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