Updated Validation Reports for Released PDB Structures

Updated validation reports for all X-ray, NMR, and 3DEM structures released in the PDB archive are now available. Of particular importance for cryo-EM, the updated report format includes EM map analysis, and fit of EM model to its map volume. FSC curves are also included to compare reported and estimated resolution, where either half maps or FSC data was uploaded.

The updates also include new percentile statistics reflecting the state of the PDB archive on December 31, 2019 and calculated map coefficients used for validation report generation.

The updated reports are accessible from the following FTP sites:

• 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 snapshot of the previous version on June 10th 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 in Validation Task Forces.

In addition to recently introduced carbohydrate section and 2D Symbol Nomenclature For Glycan (SNFG) images for oligosaccharides from the carbohydrate remediation project, these reports now incorporate visualization of ligand validation and model fit to electron density maps for X-ray ligands. These include 2-dimensional diagrams of ligands, highlighting geometric validation criteria and, for structures determined by crystallography, 3-dimensional views of electron density.

Validation reports are provided to depositors through OneDep - the wwPDB portal for 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 (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 at wwpdb.org.

Source: wwPDB News