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Experimental Phasing: Substructure Solution and Density Modification as Implemented in SHELX

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Protein Crystallography

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1607))

Abstract

This chapter describes experimental phasing methods as implemented in SHELX. After introducing fundamental concepts underlying all experimental phasing approaches, the methods used by SHELXC/D/E are described in greater detail, such as dual-space direct methods, Patterson seeding and density modification with the sphere of influence algorithm. Intensity differences from data for experimental phasing can also be used for the generation and usage of difference maps with ANODE for validation and phasing purposes. A short section describes how molecular replacement can be combined with experimental phasing methods. The second half covers practical challenges, such as prerequisites for successful experimental phasing, evaluation of potential solutions, and what to do if substructure search or density modification fails. It is also shown how auto-tracing in SHELXE can improve automation and how it ties in with automatic model building after phasing.

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Acknowledgments

I would like to thank Airlie McCoy and George M. Sheldrick for fruitful discussions. This work was supported by the European Union FP7 Marie-Curie IEF grant “SOUPINMYCRYSTAL” (grant No. 330033).

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Authors and Affiliations

  1. Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany

    Andrea Thorn

  2. Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK

    Andrea Thorn

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  1. Andrea Thorn
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Correspondence to Andrea Thorn .

Editor information

Editors and Affiliations

  1. Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland, USA

    Alexander Wlodawer

  2. Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, Illinois, USA

    Zbigniew Dauter

  3. Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland

    Mariusz Jaskolski

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Thorn, A. (2017). Experimental Phasing: Substructure Solution and Density Modification as Implemented in SHELX. In: Wlodawer, A., Dauter, Z., Jaskolski, M. (eds) Protein Crystallography. Methods in Molecular Biology, vol 1607. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7000-1_15

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  • DOI: https://doi.org/10.1007/978-1-4939-7000-1_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6998-2

  • Online ISBN: 978-1-4939-7000-1

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