PDBsum entry 2q47

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Structural genomics, unknown function PDB id
Protein chains
151 a.a.
SO4 ×4
Waters ×60

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Key reference
Title Ensemble refinement of protein crystal structures: validation and application.
Authors E.J.Levin, D.A.Kondrashov, G.E.Wesenberg, G.N.Phillips.
Ref. Structure, 2007, 15, 1040-1052. [DOI no: 10.1016/j.str.2007.06.019]
PubMed id 17850744
X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.
Figure 2.
Figure 2. Examples of Anharmonic Residue Probability Distributions for the Simulated Single- and Multiple-Conformer Models
The panels on the left show images of the electron density maps generated from the MD simulations of 1Q4R, along with a stick representation of the final 16-conformer model. The panels on the right show, for the red residues, the histograms of the projections of the simulation coordinates along the first principal components (shown in black), as well as the probability density functions calculated from the 1-conformer (red) and 16-conformer (blue) models along the same axis.
Figure 6.
Figure 6. Effect of Observation-to-Parameter Ratio on the Improvement in R[free] from Ensemble Refinement
The decrease in the R[free] value between the initial R[free] value and the R[free] value of the best-performing multiple-conformer model for the 50 experimental structures is plotted as a function of the ratio of the number of reflections used in the refinement to the number of atoms in the original one-conformer structure.
The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2007, 15, 1040-1052) copyright 2007.
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