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J Mol Biol. 2014 Feb 20;426(4):980-93. doi: 10.1016/j.jmb.2013.11.014. Epub 2013 Nov 21.

Electron density sharpening as a general technique in crystallographic studies.

Author information

1
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
2
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA. Electronic address: yong.xiong@yale.edu.

Abstract

Sharpening is a powerful method to restore the details from blurred electron density in crystals with high overall temperature factors (B-factors). This valuable technique is currently not optimally used because of the uncertainty in the scope of its application and ambiguities in practice. We performed an analysis of ~2000 crystal data sets deposited in the Protein Data Bank and show that sharpening improves the electron density map in many cases across all resolution ranges, often with dramatic enhancement for mid- and low-resolution structures. It is effective when used with either experimental or model phases without introducing additional bias. Our tests also provide a practical guide for optimal sharpening. We further show that anisotropic diffraction correction improves electron density in many cases but should be used with caution. Our study demonstrates that a routine practice of electron density sharpening may have a broad impact on the outcomes of structural biology studies.

KEYWORDS:

ADP; B-factor sharpening; CRF; FOM; MBP; MR; SA; anisotropic correction; atomic displacement parameter; automated model building; corticotropin-releasing factor; figure of merit; maltose binding protein; model-bias tolerance; molecular replacement; phase error tolerance; simulated annealing

PMID:
24269527
DOI:
10.1016/j.jmb.2013.11.014
[Indexed for MEDLINE]

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