Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement

By J. Headd, Nathaniel Echols, Pavel V. Afonine, Nigel W. Moriarty, R. Gildea, Paul D. Adams. 2014

26 citations recorded by the source corpus.

Flexible torsion angle-based NCS restraints have been implemented in phenix.refine, allowing improved model refinement at all resolutions. Rotamer correction and rotamer consistency checks between NCS-related amino-acid side chains further improve the final model quality.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, background): “Torsion-based restraints are generally preferred because they require little or no manual intervention to account for common features such as domains that are very similar in structure but differ in relative orientation (Headd et al., 2014).”
Real-space refinement in PHENIX for cryo-EM and crystallography (2018, background): “…of related copies (NCS in the case of crystallography), restraints on secondary structure, and restraints to one or more external reference models (Headd et al., 2012, 2014). phenix.real_space_refine can use the following extra restraints: - Distance and angle restraints on hydrogen bond patterns…”
Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, methodology): “Such structural information has also been exploited in a similar way by other software packages (Headd et al., 2014, 2012; Schröder et al., 2010; Sheldrick, 2015; Smart et al., 2012).”
Programming new geometry restraints: parallelity of atomic groups (2015, background): “…restraint target, the sum in equation (1), is the sum of contributions from all restraint types If additional information about the molecule or its environment is available and deemed necessary to use, additional terms can be added to equation (22) (Echols et al. , 2010; Headd et al. , 2012, 2014).”