Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.

ABSTRACT: The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Automated gradient refinement is an effective method to achieve this goal, but real-space intervention is most often required in order to adequately address problems detected by structure-validation software. In order to improve the existing protocol, automated re-refinement was combined with structure validation and difference-density peak analysis to produce a catalogue of problems in PDB entries that are amenable to automatic correction. It is shown that re-refinement can be effective in producing imp

SUBMITTER: Joosten RP 

PROVIDER: S-EPMC2631631 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature