Considerations for the refinement of low-resolution crystal structures.

By B. Delabarre, A. Brunger. 2006

73 citations recorded by the source corpus.

It is often assumed that crystal structures have to be obtained at sufficiently high resolution in order to perform macromolecular refinement. In several recent structures, the threshold of what is considered ;acceptable' has been pushed to lower diffraction resolutions. Here, considerations and modifications to standard refinement protocols are described that were used to solve and refine a particular set of low-resolution structures for the ATPase p97/VCP. It was found that reasonable R(free) values and good geometry can be achieved upon refinement that includes experimental phase information along with judicious use of restraints at diffraction limits as low as 4.7 A. At this resolution, the topology and the backbone-chain trace are mostly defined, some side-chain positions can be unambiguously assigned and ligands within known binding sites can be identified. Furthermore, large conformational changes can be discerned when structures in different states are available, information that is not easily obtainable by other means.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “This improves the data-to-parameter ratio at low resolution and therefore reduces the risk of overfitting (DeLaBarre & Brunger, 2006; for a practical example, see Braig et al., 1995; it has been noted that nearly half of the low-resolution structures in the wwPDB contain NCS copies; see, for…”
Automated map sharpening by maximization of detail and connectivity (2018, methodology): “…feature-enhanced maps (FEM, Afonine et al., 2015) and the model-building software Coot (Emsley et al., 2010) use maximization of the kurtosis of a map to choose an overall sharpening Bsharpen (an exponential factor applied to Fourier terms, cf. DeLaBarre and Brunger, 2006; Wlodawer et al., 2008).”
Blind deconvolution in scientific imaging & computational photography (2011, methodology): “For BD of single photographs, Fergus et al. (2006) combined the variational approach of Miskin and MacKay (2000) with natural image statistics (Field, 1994).”
FEM: feature-enhanced map (2014, background): “Other empirical approaches exist (DeLaBarre & Brunger, 2006).”
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta (2016, background): “Furthermore, such model building and refinement is challenging and error prone ( DeLaBarre and Brunger, 2006 ; Brunger et al., 2009 ).”
Version 1.2 of the Crystallography and NMR system (2007, methodology): “Thermal factor sharpening of electron density maps Thermal (' B ')-factor sharpening is a useful tool for enhancement of low-resolution map”