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IUCrJ. 2014 May 30;1(Pt 4):213-20. doi: 10.1107/S2052252514009324. eCollection 2014 Jul 1.

The PDB_REDO server for macromolecular structure model optimization.

Author information

1
Division of Biochemistry, Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
2
Structural Studies Division, MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0HQ, England.

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 [Read et al. (2011 ▶), Structure, 19, 1395-1412]. The PDB_REDO procedure 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 for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallo-graphers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts 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.

KEYWORDS:

PDB_REDO; model optimization; validation

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