Assessing PDB structure quality

The wwPDB has released Validation Reports for all X-ray crystal structures available in the PDB archive. 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. They summarise the quality of a 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.

 

The validation-related files for individual X-ray PDB entries can be accessed through the PDBe ftp site. The reports have also been integrated into PDBe structure entry pages. If you go to the summary page of an X-ray PDB entry (for instance: http://pdbe.org/1cbs) you will see the "percentile sliders" plot displayed in the PDBportfolio widget on the right of the page. The legend of the percentile-slider plot contains a direct link to the validation report PDF; in this case http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf).

Validation metric chart

The percentile-slider provides at-a-glance summary information that compares the quality of a model with that of other models in the archive.

A full report (which lists all outliers for many of the validation criteria), an image file of the percentile-slider plot, and an XML file with all validation data in machine-readable form, can be downloaded from a PDBe X-ray structure entry page, either by clicking the "Downloads" link in the menu on the left, or directly by going to a URL of the form: http://pdbe.org/1cbs/downloads


Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page of your favourite X-ray PDB entry, e.g.: http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs


Please send any comments, questions or suggestions on the new style validation reports to validation@mail.wwpdb.org.