[3dem] Updated Validation Reports for Released PDB and EMDB Entries

[Justin Flatt]

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 [1] 
and MolProbity updates, new Q-score percentile [2] 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://urldefense.com/v3/__https://files.wwpdb.org/pub/pdb/validation_reports/__;!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTMF0s1UI$  (wwPDB)
  	* https://urldefense.com/v3/__https://files.rcsb.org/pub/pdb/validation_reports/__;!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTF3g6QtG$  (RCSB PDB)
  	* https://urldefense.com/v3/__ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/__;!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTAYBBif7$  (PDBe)
  	* https://urldefense.com/v3/__https://files.pdbj.org/pub/pdb/validation_reports/__;!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTF3LTU_c$  (PDBj)

A snapshot of the previous version on 20260415 is archived at RCSB PDB 
[3] and PDBj [4].

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 [5].

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 
[6] and the web service API [7] 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 [5].

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 [8].

Your feedback, comments, and questions are welcome at 
validation at mail.wwpdb.org.

On behalf of the wwPDB,

Justin Flatt

Links:
------
[1] 
https://urldefense.com/v3/__https://www.wwpdb.org/validation/2017/XrayValidationReportHelp*fit_protein_na_chains__;Iw!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTJZ00dMY$ 
[2] https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2025*68c9b3a1829c3fea8eaf394d__;Iw!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTMIvIwzH$ 
[3] https://urldefense.com/v3/__https://pdbsnapshots.s3.us-west-2.amazonaws.com/index.html*20260415/__;Iw!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTE37BAX-$ 
[4] https://urldefense.com/v3/__https://snapshots.pdbj.org/20260415/__;!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTAwGlxDa$ 
[5] https://urldefense.com/v3/__https://www.wwpdb.org/task/validation-task-forces__;!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTEKAFQMn$ 
[6] https://urldefense.com/v3/__http://validate.wwpdb.org/__;!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTDahL7ZX$ 
[7] 
https://urldefense.com/v3/__https://www.wwpdb.org/validation/onedep-validation-web-service-interface__;!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTBTHLdq-$ 
[8] https://urldefense.com/v3/__https://www.wwpdb.org/validation/validation-reports__;!!Mih3wA!HkLb90EP0beILnR3Shs1w6hFNbfvoTDEI1NvLfPUc6Ubb11lBNcJzjcOg44J2GpfF6yXxEyz13UeXDLdTKLp4QMp$ 
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