P212121

PDB Structure Quality is a website that separates variables that are often correlated during crystallographic data processing and refinement. The paper entitled, Quality of protein crystal structures, is quite good and brings to light a couple of interesting points 1) the higher the impact factor of the journal the lower the quality of structures and 2) PDB quality has not significantly changed over time. If a macromolecular structure at given resolution was deposited in 1997, it is comparable to one published in 2007.

The database is current as of Nov 17, 2008, so the most recent structures will not be present.

As a heads up, the paper and website are not the same (as stated on their website):
Note: The number of independent and dependent variables has been expanded in this analysis compared to the published literature. Independent variables describing the crystal have been mined from the available structures. Those variables that were missing have been multiply imputed.

The site also has a PDB Structure Quality prediction tool to calculate the R-factor, R-free, the occupancy-weighted B-value, and the ramachandran violation percentage. As stated on their site, “This task allows a crystallographer to determine what validation metrics they should obtain at the end of refinement. If the refined validation metrics are not as good as those predicted, then further model building and refinement may be warranted.” Sweet.