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Molecules 2018, 23(3), 610; https://doi.org/10.3390/molecules23030610

An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains

1
Department of Mathematics and Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
2
Department of Computer Science, Old Dominion University; Norfolk, VA 23529, USA
*
Author to whom correspondence should be addressed.
Received: 22 December 2017 / Revised: 23 February 2018 / Accepted: 27 February 2018 / Published: 8 March 2018
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Abstract

Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2–4 Å resolutions. The results show that the normalized probability density function of block lengths is similar between the X-ray data set and the cryo-EM data set for most of the residue types, but differences were observed for ARG, GLU, ILE, LYS, PHE, TRP, and TYR for which conformations with certain shorter block lengths are more likely to be observed in the cryo-EM set with 2–4 Å resolutions. View Full-Text
Keywords: protein; structure; cryo-electron microscopy; validation; statistics; X-ray; crystallography; side chain protein; structure; cryo-electron microscopy; validation; statistics; X-ray; crystallography; side chain
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Chen, L.; He, J.; Sazzed, S.; Walker, R. An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains. Molecules 2018, 23, 610.

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