All validation reports for released PDB and EMDB entries have been updated and are now available with recalculated percentiles. In addition, validation reports now include new percentile statistics reflecting the state of the PDB archive on December 31, 2025, EDS and MolProbity updates, new Q-score percentile information, and ligand validation improvements.
Ligand validation improvements were made in response to feedback from Global Phasing Ltd., reporting that wwPDB validation software queries of the CSD via Mogul returned insufficient results for such common moieties as adenine, leading to an incorrect rendering of geometric quality in the buster-report-like diagrams. This was traced to a mismatch in aromaticity specifications between wwPDB validation software and Mogul, that has now been updated. In addition, a depiction of non-carbon atoms by grey balls has been added to these diagrams.
The updated reports are accessible from:
- https://files.wwpdb.org/pub/pdb/validation_reports/ (wwPDB)
- https://files.rcsb.org/pub/pdb/validation_reports/ (RCSB PDB)
- ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe)
- https://files.pdbj.org/pub/pdb/validation_reports/ (PDBj)
A snapshot of the previous version on 20260415 is archived at RCSB PDB and PDBj.
These updated wwPDB validation reports provide an assessment of structure quality using widely accepted standards and criteria, recommended by community experts serving on Validation Task Forces.
Validation reports are provided to depositors through OneDep--the wwPDB portal for validation, deposition and biocuration of structure data. 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 (VTF) for X-ray, NMR, EM, and as we collect feedback from depositors and users.
The wwPDB partners strongly encourage journal editors and referees to request reports from authors as part of the manuscript submission and review process, as 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. Reports are date-stamped, display the wwPDB logo, and represent standardized wwPDB validation.
Further information and sample validation reports are available.
Your feedback, comments, and questions are welcome at validation@mail.wwpdb.org.
