Dataset Information

CCP4i2: the new graphical user interface to the CCP4 program suite.

ABSTRACT: The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition, CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures.

SUBMITTER: Potterton L

PROVIDER: S-EPMC5947771 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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CCP4i2: the new graphical user interface to the CCP4 program suite.

Potterton Liz L Agirre Jon J Ballard Charles C Cowtan Kevin K Dodson Eleanor E Evans Phil R PR Jenkins Huw T HT Keegan Ronan R Krissinel Eugene E Stevenson Kyle K Lebedev Andrey A McNicholas Stuart J SJ Nicholls Robert A RA Noble Martin M Pannu Navraj S NS Roth Christian C Sheldrick George G Skubak Pavol P Turkenburg Johan J Uski Ville V von Delft Frank F Waterman David D Wilson Keith K Winn Martyn M Wojdyr Marcin M

Acta crystallographica. Section D, Structural biology 20180201 Pt 2

The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical ...[more]

PMID: 29533233

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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

CCP4i2: the new graphical user interface to the CCP4 program suite.

Publications

CCP4i2: the new graphical user interface to the CCP4 program suite.

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