Ryan McGreevy, Abhishek Singharoy, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo
Perozo, and Klaus Schulten.
xMDFF: Molecular dynamics flexible fitting of low-resolution
X-Ray structures.
Acta Crystallographica D, 70:2344-2355, 2014.
(PMC: PMC4157446)
MCGR2014
X-ray crystallography remains the most dominant method for solving atomic structures.
However, for relatively large systems, availability of only medium to low-resolution
diffraction data often limits the determination of all-atom details. We have developed a
new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining
structures from such low-resolution crystallographic data. xMDFF employs a real-space
refinement scheme that flexibly fits atomic models into an iteratively updating electron
density map. It addresses significant large-scale deformations of the initial model to fit the
low-resolution density, as is tested with synthetic low-resolution maps of D ribose binding
protein. xMDFF has been successfully applied to re-refine six low-resolution protein
structures of varying sizes that were already submitted to the Protein Data Bank. Finally, via
systematic refinement of a series of data from 3.6 to 7 Åresolution, xMDFF refinements
together with electrophysiology experiments confirmed the first all-atom structure of a
voltage sensing protein Ci-VSP.
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