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Licensed Unlicensed Requires Authentication Published by De Gruyter (O) July 28, 2010

Phase determination in protein x-ray crystallography at low resolution – 6.0 Å Data from rubredoxin via the pseudoatom glob approximation

Abstract

With a re-scaled pseudoatom scattering factor approximation to the Fourier transform of globular density units in the protein, the crystal structure of rubredoxin was determined from experimental x-ray diffraction data by direct methods at 6 Å resolution. The Sayre equation expanded a relatively small basis set and screening criteria, such as density flatness and a Patterson correlation coefficient, selected the best of several possible solutions. In the two-dimensional determination, principal peak positions were located in the maps, giving a mean phase error of 57.6° for all 17 hk0 reflections after two cycles of Fourier refinement. In the three-dimensional determination, the initial phase set could be compared to the original x-ray model by a mean deviation of 85.3° for all 127 hkl reflections but only 54.3° for the 23 most intense maxima. Refinement improved the overall fit (mean error: 77.4° but only 62.3° for the 23 most intense reflections). Because the phase value of the most intense reflection is greatly improved, the electron density map is closer to that of the actual structure. However, a priori imposition of globular substructure causes the 3-D density map to become discontinuous. The success of this phasing attempt is quite surprising for an example where the solvent space contains a high concentration of ammonium sulfate where the contrast at low resolution should be reversed.

Published Online: 2010-7-28
Published in Print: 1999-10-1

© 2015 Oldenbourg Wissenschaftsverlag GmbH, Rosenheimer Str. 145, 81671 München

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