Tools for macromolecular model building and refinement into electron cryo‐microscopy reconstructions. (1st January 2015)

• Record Type: Journal Article
• Authors: Brown, Alan; Long, Fei; Nicholls, Robert A.; Toots, Jaan; Emsley, Paul; Murshudov, Garib
• Is Part Of: Acta crystallographica. Volume 71:Part 1(2015:Jan.)
• Page Start: 136
• Page End: 153
• Publication Date: 2015-01-01
• Subjects: Biomolecules -- Structure -- Periodicals; Physical biochemistry -- Periodicals; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; 572
• DOI: 10.1107/S1399004714021683
• Languages: English
• ISSNs: 0907-4449

Abstract

<abstract abstract-type="main" xml:lang="en"> <title> <x xml:space="preserve">Abstract</x> </title> <p>The recent rapid development of single‐particle electron cryo‐microscopy (cryo‐EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all‐atom models are described. The <italic>BALBES</italic> database has been repurposed as a tool for identifying protein folds from density maps. Modifications to <italic>Coot</italic>, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. <italic>REFMAC</italic> has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, <italic>ProSMART</italic> has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, <italic>LIBG</italic>, has been developed to generate nucleic acid base‐pair and parallel‐plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in <italic>Coot</italic>, and these restraints have been applied to both real‐space refinement in <italic>Coot</italic> and reciprocal‐space refinement in <italic>REFMAC</italic>.</p> </abstract>