Validation reports available for all X-ray structures in the PDB

The Worldwide Protein Data Bank (wwPDB) partners are pleased to announce that validation reports for all X-ray crystal structures in the PDB archive are now publicly available.

The validation reports provide at-a-glance summary information that compares the quality of a model with that of other models in the archive.

  The reports contain residue-property plots. Residues are color-coded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dot above a residue indicates a poor fit to the electron density (RSRZ>2).

'The new validation reports are sure to become an indispensable resource for all X-ray crystallographers. Most importantly, we hope they will be really useful for all the end users of structural models, who increasingly need to critically assess and compare PDB entries,' said Anastassis Perrakis, Netherlands Cancer Inst., whose research focuses both on analysing macromolecular structures relevant for cancer, and also on developing the tools needed to decipher these structures.

The reports implement the recommendations of a large group of community experts on validation and include the results of geometric checks, structure-factor assessment and ligand validation. The reports include results from tried and tested software including MolProbity, Xtriage, Mogul, EDS and various CCP4 programs. They summarise the quality of the structure and highlight specific concerns by considering the coordinates of the model, the diffraction data and the fit between the two. Easily interpretable summary information that compares the quality of a structure with that of other structures in the archive is also provided.

Validating structures prior to publication and deposition

The new X-ray structure-validation reports have been provided to depositors as part of the structure-annotation process since August 2013. More recently, a stand-alone wwPDB X-ray structure validation server was launched (http://wwpdb-validation.wwpdb.org/). The server allows crystallographers to check early, intermediate and near-final models on demand and helps identify any potential problems that need addressing prior to structure analysis, publication and deposition.

'The stand-alone validation server will run exactly the same validation tests that have recently been introduced for the annotation of new depositions,' says Randy Read of Cambridge U. Read chairs the wwPDB X-ray Validation Task Force (VTF) that has produced detailed recommendations to the wwPDB about how macromolecular crystal structures should be validated ^[1]. 'With the stand-alone server, crystallographers won't have any last-minute surprises when they deposit their structures just before submitting the paper,' Read adds.

Accessing validation reports for archived structures

Validation reports for X-ray structures archived in the PDB are accessible from the following FTP sites:

ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ (wwPDB)

ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe)

ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj)

The reports have been developed in the context of a larger initiative, the new wwPDB Deposition and Annotation system (http://wwpdb.org/system_info.html), which was created to unify the annotation tools and practices used across all wwPDB deposition centres and for all common structure-determination methods.

[1] Read R. J., Adams P. D., Arendall III W. D., Brünger A. T., Emsley P., Joosten R.P., Kleywegt G. J., Krissinel E. B., Lütteke T., Otwinowski Z., Perrakis A., Richardson J. S., Sheffler W. H., Smith J. L., Tickle I. J., Vriend G. and Zwart P. H. (2011). A new generation of crystallographic validation tools for the Protein Data Bank. Structure, 19, 1395-1412. DOI: 10.1016/j.str.2011.08.006.