Date Published: June 01, 2018
Publisher: International Union of Crystallography
Author(s): Pavel V. Afonine, Billy K. Poon, Randy J. Read, Oleg V. Sobolev, Thomas C. Terwilliger, Alexandre Urzhumtsev, Paul D. Adams.
A description is provided of the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite and its application to the re-refinement of cryo-EM-derived models.
Improvements in the cryo-electron microscopy (cryo-EM) technique have led to a rapid increase in the number of high-resolution three-dimensional reconstructions that can be interpreted with atomic models (Fig. 1 ▸). This has prompted a number of new developments in PHENIX (Adams et al., 2010 ▸) to support the method, from model building (Terwilliger, Adams et al., 2018 ▸), map improvement (Terwilliger, Sobolev et al., 2018 ▸) and refinement (Afonine et al., 2013 ▸) to model validation (Afonine et al., 2018 ▸). In this manuscript, we focus on atomic model refinement using a map (primarily cryo-EM, but the same algorithms and software are also applicable to crystallographic maps).
Refinement of an atomic model against a map is increasingly important as the technique of cryo-EM rapidly develops. We have described the algorithms implemented in a new PHENIX tool, phenix.real_space_refine, that was specifically designed to perform such real-space refinements. RSR is a natural choice for cryo-EM, unlike crystallography, where real-space methods are complementary to Fourier-space refinement and are somewhat limited since crystallographic maps are almost always model-biased. Nevertheless, while this work was inspired by rapid advances in the field of cryo-EM and the increasing number of three-dimensional reconstructions that allow atomic models to be refined (as opposed to rigid-body docked), the implementation is not limited to cryo-EM and crystallographic maps can also be used.