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PDBe Validation for Release

A PDB ID code will be issued only after the depositor gives approval to release his/her entry within the time frame allowed by the IUCR and wwPDB guidelines.

PDBe staff will process the deposited entry. This processing will include standardization of nomenclature, annotations, and data representation. Special processing instructions will be addressed at this time. Most of this work covers issues not fully delegated to software.

For entries for which structure factors have been provided, these structure factors will be validated against the deposited coordinates. These checks include validation using the CCP4 program SFCHECK, and an in-house customized version of the Uppsala Electron Density Software (EDS). The results of these validation checks will be made available to the depositor.

Listed below are a series of checks that will be done on an entry as part of the submission process. The first checks will be used to ensure that entries with obvious deficiencies are not released (e.g., duplicate atom records). The other checks will be used to add annotations to the entry.

The following tests will be done on the entry as part of the submission process. Results of the tests will be provided to the depositor who can then take appropriate action given the options outlined below before a PDB ID code is issued.

Diagnostics requiring corrections and re-submission of coordinate data.

  • More than one polypeptide or nucleotide chain assigned the same chain name.
  • Heterogen group specified by HET and FORMUL records not present in the ATOM/HETATM records.
  • More than 10% of the atoms involved in unusually close crystal packing interactions (this check will also cover the case for which a non-standard space group setting was used and the correct set of symmetry operators was not provided).
  • Violation of atom nomenclature for standard amino and nucleic acids.
  • Duplicate ATOM or HETATM records in the same residue with the same atom name or the same coordinates.
  • ATOM/HETATM records not formatted as described in the PDB Contents Guide

Diagnostics requiring annotations and/or comments to be provided by the depositors if the data are not corrected. The PDB will insert a CAVEAT record before release.

  • For polypeptides, phi-psi angles for more than 20% of the residues are outside the allowable region.
  • Unexpected chirality at C-alpha center.

The following diagnostics are normally used by PDB staff to take a closer look at the data because, by experience, we have found that they may be indicative of unusual structures or possible problems.

We will present this information to the depositor and the list will also be included in a file containing the output of our checking runs to be made available to the users. The depositor may, of course, modify the coordinate file during the submission process to correct for possible errors before giving final approval to release the data.

  • RMSD of bond lengths greater than 0.08 Ångstroms from ideal values.
  • RMSD of bond angles greater than 5.0 degrees.
  • Breaks in the chain (e.g., due to disorder).
  • Differences between amino acid sequences given by the ATOM records and those given in the appropriate sequence database entry.
  • Amino acid sequences not reported in any sequence database.
  • CIS-peptides and peptide bonds that deviate significantly from the expected trans conformation.
  • Individual bond lengths differing by more than 0.1 Ångstroms from standard values.
  • Individual bond angles differing by more than 15 degrees from standard values.
  • Atoms too close to symmetry axes.
  • Atoms involved in unusually close crystal packing interaction.
  • Occupancy less than or equal to 0.0 or occupancy greater than 1.0.
  • Missing residues, missing atoms.
  • Atom occupancies less than 1.0 and for which no alternate location ATOM record is provided.
  • Thermal factors greater than 100 Å**2.
  • Unexpected deviations from planarity.
  • Non-standard SCALE matrix.
  • OXT atom record in the middle of a chain (flagged as extra atom) typically occurring before a gap in the coordinates.
  • R value greater than 30%.
  • Free-R value greater than 35%.
  • Free-R and R value differ by more than 10%.
  • RMSD between atoms related by an NCS MTRIX record is greater than 3.0 Ångstroms.

Tests which are valid only for diffraction experiments will not be applied to entries reporting NMR experiments or model building studies.

Heterogen groups will be checked against the current PDB Het Dictionary. The only check that will be done at this stage of the processing is to see if the HET ID and the atom nomenclature used for a group is consistent with the dictionary (e.g., is the GLC group in the coordinate file a glucose molecule as given in the PDB Het Dictionary and are the atoms properly named?). Groups that are not in the dictionary and for which there is no conflict on the HET ID code will be accepted as is and will be checked and standardized as part of the regular processing to be done after the entry is loaded.

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