Access Structure Quality Metrics


wwPDB Validation Reports provide an assessment of the quality of a structure and highlight specific concerns by considering the model coordinates, experimental data, and fit between the two.

RCSB PDB News Image

RCSB PDB Structure Summary pages contain the “slider” graphic from these reports that provides a visual summary and also link to the full PDF report.

Users can also access the PDF and XML versions of the Validation Report from the "Display Files" menu.

RCSB PDB News Image

The 3D NGL viewer maps report information onto the structure. Clashes can be displayed as pink disks, and the full structure can be shown using “Geometry Quality” and “Density Fit” coloring schemes. Detailed information about this feature is available.

RCSB PDB News ImageHydrolases colored using the “Density Fit” scheme. On the left, PDB structure 3wy6 with a generally good fit; on the right, PDB structure 3wyz which has areas of more problematic fit.

wwPDB Validation Reports use widely-accepted standards and criteria, recommended by community experts serving in Validation Task Forces. Reports are provided to data depositors during OneDep validation, deposition and biocuration; shared with journal editors and referees as part of manuscript submission and review; and distributed by the wwPDB at the time of data release.

For more information:

Validation of Structures in the Protein Data Bank (2017) Structure 25: 1916-1927 doi: 10.1016/j.str.2017.10.009.

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