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The CCP4 suite: integrative software for macromolecular crystallography.

ABSTRACT: The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

SUBMITTER: Agirre J

PROVIDER: S-EPMC10233625 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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The CCP4 suite: integrative software for macromolecular crystallography.

Agirre Jon J Atanasova Mihaela M Bagdonas Haroldas H Ballard Charles B CB Baslé Arnaud A Beilsten-Edmands James J Borges Rafael J RJ Brown David G DG Burgos-Mármol J Javier JJ Berrisford John M JM Bond Paul S PS Caballero Iracema I Catapano Lucrezia L Chojnowski Grzegorz G Cook Atlanta G AG Cowtan Kevin D KD Croll Tristan I TI Debreczeni Judit É JÉ Devenish Nicholas E NE Dodson Eleanor J EJ Drevon Tarik R TR Emsley Paul P Evans Gwyndaf G Evans Phil R PR Fando Maria M Foadi James J Fuentes-Montero Luis L Garman Elspeth F EF Gerstel Markus M Gildea Richard J RJ Hatti Kaushik K Hekkelman Maarten L ML Heuser Philipp P Hoh Soon Wen SW Hough Michael A MA Jenkins Huw T HT Jiménez Elisabet E Joosten Robbie P RP Keegan Ronan M RM Keep Nicholas N Krissinel Eugene B EB Kolenko Petr P Kovalevskiy Oleg O Lamzin Victor S VS Lawson David M DM Lebedev Andrey A AA Leslie Andrew G W AGW Lohkamp Bernhard B Long Fei F Malý Martin M McCoy Airlie J AJ McNicholas Stuart J SJ Medina Ana A Millán Claudia C Murray James W JW Murshudov Garib N GN Nicholls Robert A RA Noble Martin E M MEM Oeffner Robert R Pannu Navraj S NS Parkhurst James M JM Pearce Nicholas N Pereira Joana J Perrakis Anastassis A Powell Harold R HR Read Randy J RJ Rigden Daniel J DJ Rochira William W Sammito Massimo M Sánchez Rodríguez Filomeno F Sheldrick George M GM Shelley Kathryn L KL Simkovic Felix F Simpkin Adam J AJ Skubak Pavol P Sobolev Egor E Steiner Roberto A RA Stevenson Kyle K Tews Ivo I Thomas Jens M H JMH Thorn Andrea A Valls Josep Triviño JT Uski Ville V Usón Isabel I Vagin Alexei A Velankar Sameer S Vollmar Melanie M Walden Helen H Waterman David D Wilson Keith S KS Winn Martyn D MD Winter Graeme G Wojdyr Marcin M Yamashita Keitaro K

Acta crystallographica. Section D, Structural biology 20230530 Pt 6

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graph ...[more]

PMID: 37259835

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Project description:Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein-protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium-low resolution.

Dataset Information

The CCP4 suite: integrative software for macromolecular crystallography.

Publications

The CCP4 suite: integrative software for macromolecular crystallography.

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