ThePDB_REDOserver for macromolecular structure model optimization

Abstract

The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Readet al.(2011),Structure,19, 1395–1412]. ThePDB_REDOprocedure aims for `constructive validation', aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server forPDB_REDOhas been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure inREFMACand partial model rebuilding. The goal of the web server is to help practicing crystallographers to improve their model prior to submission to the PDB. For this, additional steps were implemented in thePDB_REDOpipeline, both in the refinement procedure,e.g.testing of resolution limits andk-fold cross-validation for small test sets, and as new validation criteria,e.g.the density-fit metrics implemented inEDSTATSand ligand validation as implemented inYASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generatedCootscripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB.