Overview of refinement procedures within REFMAC5: utilizing data from different sources. Issue 3 (5th April 2018)

• Record Type: Journal Article
• Authors: Kovalevskiy, Oleg; Nicholls, Robert A.; Long, Fei; Carlon, Azzurra; Murshudov, Garib N.
• Is Part Of: Acta crystallographica. Volume 74:Issue 3(2018)
• Page Start: 215
• Page End: 227
• Publication Date: 2018-04-05
• Subjects: REFMAC5 -- ProSMART -- LORESTR -- NMR restraints -- refinement; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; Molecular biology -- Periodicals; Molecular structure -- Periodicals; Biomolecules -- Structure -- Periodicals; Cytology -- Periodicals; Biomolecules -- Structure; Crystallography; Cytology; Molecular biology; Molecular structure; X-ray crystallography; Periodicals; 548
• DOI: 10.1107/S2059798318000979
• Languages: English
• ISSNs: 2059-7983

Abstract

Abstract : Here, a macromolecule‐centred approach to three‐dimensional structure determination as implemented in REFMAC 5 is considered. The use of restraints to transfer chemical and structural information during macromolecular refinement, and how different sources of information can be combined in order to achieve models that are more consistent with data derived from a variety of experimental techniques, including macromolecular crystallography, cryo‐EM and NMR spectroscopy, are discussed. Abstract : Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters ( B factors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors. A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. If the observation‐to‐parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC 5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary‐structure formation and even data obtained using different experimental methods, for example NMR. The refinement procedure also generates the `best' weighted electron‐density maps, which are useful for further model (re)building. Here, the refinement of macromolecular structures using REFMAC 5 and related tools distributed as part of the CCP 4 suite is discussed.