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A density-modification method for the improvement of poorly resolved protein electron-density maps

A density-modification method for the improvement of poorly resolved protein electron-density maps An efficient computer procedure has been developed for the extraction of regions of contiguous, well-connected high density from a three-dimensional electron-density map. This procedure may be used to generate an extended model volume, from a smaller volume based on a starting atomic model. The starting model may, for example, only include main-chain atoms for a protein, or may omit uninterpretable segments of chain. The procedure may also be used to extract regions of contiguous density where no model exists. The extended model volume is used to produce a properly scaled model electron density. Calculated structure factors are obtained from the scaled model electron density by fast Fourier transform, and combined, with appropriate weights, with the existing phase information to give improved phase angles. Calculation of a new electron-density map with the new phase angles initiates the next step of a cyclic procedure which converges rapidly. The procedure has been applied to the structure determination of tyrosyl-tRNA synthetase. It has led to identification of most of the available amino-acid sequence in the electron density, and a revised tracing of the main polypeptide chain. Evidence for improvement in phase angles is obtained from electron-density difference maps for substrate and inhibitor binding, in which a reduction in background density is observed. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Acta Crystallographica Section A: Crystal Physics, Diffraction, Theoretical and General Crystallography International Union of Crystallography

A density-modification method for the improvement of poorly resolved protein electron-density maps

A density-modification method for the improvement of poorly resolved protein electron-density maps


Abstract

An efficient computer procedure has been developed for the extraction of regions of contiguous, well-connected high density from a three-dimensional electron-density map. This procedure may be used to generate an extended model volume, from a smaller volume based on a starting atomic model. The starting model may, for example, only include main-chain atoms for a protein, or may omit uninterpretable segments of chain. The procedure may also be used to extract regions of contiguous density where no model exists. The extended model volume is used to produce a properly scaled model electron density. Calculated structure factors are obtained from the scaled model electron density by fast Fourier transform, and combined, with appropriate weights, with the existing phase information to give improved phase angles. Calculation of a new electron-density map with the new phase angles initiates the next step of a cyclic procedure which converges rapidly. The procedure has been applied to the structure determination of tyrosyl-tRNA synthetase. It has led to identification of most of the available amino-acid sequence in the electron density, and a revised tracing of the main polypeptide chain. Evidence for improvement in phase angles is obtained from electron-density difference maps for substrate and inhibitor binding, in which a reduction in background density is observed.

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Publisher
International Union of Crystallography
Copyright
Copyright (c) 1982 International Union of Crystallography
ISSN
0567-7394
DOI
10.1107/S0567739482000059
Publisher site
See Article on Publisher Site

Abstract

An efficient computer procedure has been developed for the extraction of regions of contiguous, well-connected high density from a three-dimensional electron-density map. This procedure may be used to generate an extended model volume, from a smaller volume based on a starting atomic model. The starting model may, for example, only include main-chain atoms for a protein, or may omit uninterpretable segments of chain. The procedure may also be used to extract regions of contiguous density where no model exists. The extended model volume is used to produce a properly scaled model electron density. Calculated structure factors are obtained from the scaled model electron density by fast Fourier transform, and combined, with appropriate weights, with the existing phase information to give improved phase angles. Calculation of a new electron-density map with the new phase angles initiates the next step of a cyclic procedure which converges rapidly. The procedure has been applied to the structure determination of tyrosyl-tRNA synthetase. It has led to identification of most of the available amino-acid sequence in the electron density, and a revised tracing of the main polypeptide chain. Evidence for improvement in phase angles is obtained from electron-density difference maps for substrate and inhibitor binding, in which a reduction in background density is observed.

Journal

Acta Crystallographica Section A: Crystal Physics, Diffraction, Theoretical and General CrystallographyInternational Union of Crystallography

Published: Jan 1, 1982

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