Data Deposition/Biocuration Services and Archive Management

In 2020, 15436 experimentally-determined structures were deposited to the archive.  Data are processed by wwPDB partners RCSB PDB, PDBe, and PDBj.

Of all structures deposited this year, 81.5% were deposited with a release status of hold until publication; 13.4% were released as soon as annotation of the entry was complete; and 5.1% were held until a particular date. 79.4% of these entries were determined by X-ray crystallographic methods; 2.6% were determined by NMR methods; and 17.9% by 3DEM.

14,060 new PDB structures were released in 2020 They account for 8.1% of the year-end total holdings of 173,110 available entries. 795 SARS-CoV-2 structures were released.

In 2020, 3,827 EMDB maps were released in the PDB.

Distribution of distance restraints and violations

Distribution of dihedral-angles and violations.

wwPDB validation reports provided in OneDep now include restraints validation for NMR entries to help users identify potential discrepancies in their data.

Recommendations from the wwPDB NMR Validation Task Force (VTF) on how restraints data should be validated have been published (10.1016/j.str.2013.07.021). Since then, wwPDB has been working with the NMR community to develop the NMR Exchange Format (NEF) dictionary (10.1038/nsmb.3041) to enable validation of restraints data.

In March 2020, OneDep was configured to accept NMR experimental data (chemical shifts and restraints) as a single file, either in NMR-STAR or NEF format. Now, NMR restraints data validation has been incorporated into the wwPDB validation package. Validation Reports generated in OneDep have been extended to include NMR restraints analysis in when restraints are deposited in either NEF or NMR-STAR format.

The contents of restraints analysis in the wwPDB validation reports include conformationally restricting restraints, residual restraint violations, average number of distance and dihedral angle restraint violations per model, and distance and dihedral angle violation analysis for each model and ensemble with graphical and tabular statistics.

These features should help both depositors and users to identify potential errors in NMR data.

Additional information about validation reports for NMR entries is available.