Bringing Structure to Biology
Access Updated Validation Reports for PDB Structures
Validation reports for all PDB structures have been updated to include new percentile statistics reflecting the state of the archive on December 31st 2017 and updated versions of third-party software: CCP4/Refmac (7.0 v44), Phenix (1.13) and Mogul (2018) and CSD archive (as539be). The LLDF statistic previously used to identify ligands that do not fit electron density well has been replaced by a combination of Real-space R-factor (RSR>0.4) and Real-space correlation coefficient (RSCC<0.8). The identification of standard amino acid or nucleotide residues that do not fit the electron density well has been corrected to take into account how reliably Refmac software reproduces the R-factors reported by authors. Documentation at wwpdb.org/validation has been updated to reflect these changes.
Updated reports are accessible from:
- ftp://ftp.wwpdb.org/pub/pdb/validation_reports (wwPDB)
- ftp://ftp.rcsb.org/pub/pdb/validation_reports (RCSB PDB)
- ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports (PDBe)
- ftp://ftp.pdbj.org/pub/pdb/validation_reports (PDBj)
A copy of the previous version is archived at RCSB PDB and PDBj.
wwPDB validation reports provide an assessment of structure quality using widely accepted standards and criteria, recommended by community experts serving in the Validation Task Force. The wwPDB partners strongly encourage journal editors and referees to request them from authors as part of the manuscript submission and review process. The reports are date-stamped and display the wwPDB logo, and contain the same information, regardless of which wwPDB site processed the entry. Provision of wwPDB validation reports is already required by Nature, eLife, The Journal of Biological Chemistry, the International Union of Crystallography (IUCr) journals, FEBS journals, Journal of Immunology and Angew Chem Int Ed Engl as part of their manuscript-submission process.
Validation reports are also provided to depositors through OneDep validation, deposition and biocuration of structure data. The wwPDB partners encourage the use of the stand-alone validation server and the web service API at any time prior to data deposition. Depositors are required to review and accept the reports as part of the data submission process. Validation reports will continue to be developed and improved as we receive recommendations from the expert Validation Task Forces for X-ray, NMR, EM, and experts on ligand validation, and as we collect feedback from depositors and users.
An article focused on the structure validation reports produced by wwPDB is available: Validation of Structures in the Protein Data Bank (2017) Structure 25: 1317-1318 doi: 10.1016/j.str.2017.10.009.
Your feedback, comments, and questions are welcome at firstname.lastname@example.org.