Real-space refinement in <i>PHENIX</i> for cryo-EM and crystallography

Abstract

This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.

Keywords

Affiliated Institutions

• University of California, Berkeley US
• Centre National de la Recherche Scientifique FR
• New Mexico Consortium US
• Université de Lorraine FR
• Shanghai University CN
• Wellcome Trust GB
• Los Alamos National Laboratory US
• Lawrence Berkeley National Laboratory US
• Inserm FR
• University of Cambridge GB
• Institut de génétique et de biologie moléculaire et cellulaire FR

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