Advances in molecular‐replacement procedures: the REVAN pipeline. (1st September 2015)

• Record Type: Journal Article
• Authors: Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Mazzone, Annamaria
• Is Part Of: Acta crystallographica. Volume 71:Part 9(2015:Sep.)
• Page Start: 1856
• Page End: 1863
• Publication Date: 2015-09-01
• Subjects: Biomolecules -- Structure -- Periodicals; Physical biochemistry -- Periodicals; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; 572
• DOI: 10.1107/S1399004715012730
• Languages: English
• ISSNs: 0907-4449

Abstract

<abstract abstract-type="main" xml:lang="en"> <title> <x xml:space="preserve">Abstract</x> </title> <p>The <italic>REVAN</italic> pipeline aiming at the solution of protein structures <italic>via</italic> molecular replacement (MR) has been assembled. It is the successor to <italic>REVA</italic>, a pipeline that is particularly efficient when the sequence identity (SI) between the target and the model is greater than 0.30. The <italic>REVAN</italic> and <italic>REVA</italic> procedures coincide when the SI is >0.30, but differ substantially in worse conditions. To treat these cases, <italic>REVAN</italic> combines a variety of programs and algorithms (<italic>REMO</italic>09, <italic>REFMAC</italic>, <italic>DM</italic>, <italic>DSR</italic>, <italic>VLD</italic>, <italic>free lunch</italic>, <italic>Coot</italic>, <italic>Buccaneer</italic> and <italic>phenix.autobuild</italic>). The MR model, suitably rotated and positioned, is first refined by a standard <italic>REFMAC</italic> refinement procedure, and the corresponding electron density is then submitted to cycles of <italic>DM</italic>–<italic>VLD</italic>–<italic>REFMAC</italic>. The next <italic>REFMAC</italic> applications exploit the better electron densities obtained at the end of the <italic>VLD</italic>–EDM sections (a procedure called vector refinement). In order to make the model more similar to the target, the model is submitted to mutations, in which <italic>Coot</italic> plays a basic role, and it is then cyclically resubmitted to <italic>REFMAC</italic>–EDM–<italic>VLD</italic> cycles. The phases thus obtained are submitted to <italic>free lunch</italic> and allow most of the test structures studied by DiMaio <italic>et al.</italic> [(2011), <italic>Nature (London)</italic>, <bold>473</bold>, 540–543] to be solved without using energy‐guided programs.</p> </abstract>