PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 15983421

Optimizing statistical Shake-and-Bake for Se-atom substructure determination.

Hongliang Xu·Charles M Weeks·Herbert A Hauptman
View original source ↗Export metadata ↓

Abstract

A novel statistical approach to the phase problem in X-ray crystallography was introduced in a recent paper [Xu & Hauptman (2004), Acta Cryst. A60, 153-157]. In this approach, a new minimal function based on the statistical distribution of structure-invariant values serves as the foundation of an optimization procedure called statistical Shake-and-Bake. Favorable application of this procedure to Se-atom substructure determination depends on the choice of the statistical interval over which the function is defined. The effects of interval variation have been studied for 19 Se-atom substructures ranging in size from five to 70 Se atoms in the asymmetric unit and the results have shown an overall improvement in success rate relative to traditional Shake-and-Bake. Statistical Shake-and-Bake is being incorporated as the default optimization procedure in newly distributed versions of the SnB and BnP computer programs.

Explore related subjects

Crystallography, X-RaySeleniumSoftwareStatistics as TopicComparative StudyJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Hongliang Xu, Charles M Weeks, Herbert A Hauptman. 2005-06-24. Optimizing statistical Shake-and-Bake for Se-atom substructure determination.. https://doi.org/10.1107/s0907444905011558

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

Prediction of side-chain conformations on protein surfaces.

An approach is described that improves the prediction of the conformations of surface side chains in crystal structures, given the main-chain conformation of a protein. A key element of the methodology involves the use of the colony energy. This phenomenological term favors conformations found in frequently sampled regions, thereby approximating entropic effects and serving to smooth the potential energy surface. Use of the colony energy significantly improves prediction accuracy for surface side chains with little additional computational cost. Prediction accuracy was quantified as the percentage of side-chain dihedral angles predicted to be within 40 degrees of the angles measured by X-ray diffraction. Use of the colony energy in predictions for single side chains improved the prediction accuracy for chi(1) and chi(1+2) from 65 and 40% to 74 and 59%, respectively. Several other factors that affect prediction of surface side-chain conformations were also analyzed, including the extent of conformational sampling, details of the rotamer library employed, and accounting for the crystallographic environment. The prediction of conformations for polar residues on the surface was generally found to be more difficult than those for hydrophobic residues, except for polar residues participating in hydrogen bonds with other protein groups. For surface residues with hydrogen-bonded side chains, the prediction accuracy of chi(1) and chi(1+2) was 79 and 63%, respectively. For surface polar residues, in general (all side-chain prediction), the accuracy of chi(1) and chi(1+2) was only 73 and 56%, respectively. The most accurate results were obtained using the colony energy and an all-atom description that includes neighboring molecules in the crystal (protein chains and hetero atoms). Here, the accuracy of chi(1) and chi(1+2) predictions for surface side chains was 82 and 73%, respectively. The root mean square deviations obtained for hydrogen-bonding surface side chains were 1.64 and 1.81 A, with and without consideration of crystal packing effects, respectively.

Crystallography, X-Ray↗
PubMed2007

Double-stranded cycles: toward C84's belt region.

The reactivity of the double-stranded hydrocarbon cycle with two ether bridges (1) toward iodotrimethylsilane (TMSI) was investigated in some detail. The carbon skeleton of cycle 1 resembles the belt region of a C84 fullerene which makes it a potential precursor to the long sought after fully aromatic derivative. Upon exposure to TMSI, cycle 1 undergoes a cascade of reactions which involve different states of iodination/reduction which ultimately lead to the hydrogenated cycle 5a, whose structure was proven by single-crystal X-ray analysis. A deeper insight into mechanistic aspects of this sequence of conversions was gained by performing the reaction under dry and wet conditions, whereby the latter involved both normal and deuterated water. With the help of detailed NMR correlation studies and DFT computations, all important aspects were clarified including an unexpected selective H/D exchange at the naphthalenic moieties.

Crystallography, X-Ray↗