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Related Concept Videos

The Phase Rule01:20

The Phase Rule

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The phase rule describes the relationship between the variance (degrees of freedom), the number of components, and the number of phases in a system at equilibrium.Variance is a concept that denotes the number of independent intensive properties (properties are those that do not depend on the amount of material in the system), such as temperature, pressure, and composition, that can be altered without impacting the number of phases in equilibrium.In a single-component system, such as pure water,...
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Experimental Phasing: Substructure Solution and Density Modification as Implemented in SHELX.

Andrea Thorn1,2

  • 1Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany. andrea.thorn@web.de.

Methods in Molecular Biology (Clifton, N.J.)
|June 3, 2017
PubMed
Summary
This summary is machine-generated.

This chapter details experimental phasing methods in SHELX, covering dual-space direct methods, Patterson seeding, and density modification. It also addresses practical challenges and integrates molecular replacement for improved crystallographic structure determination.

Keywords:
Anomalous difference mapAnomalous diffractionDensity modificationDirect methodsExperimental phasingHeavy atomsMADMR-SADRIP phasingSADSubstructure search

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Area of Science:

  • Crystallography
  • Structural Biology
  • Computational Chemistry

Background:

  • Experimental phasing is crucial for determining the three-dimensional structure of molecules when direct methods or molecular replacement are insufficient.
  • Accurate structure determination is fundamental to understanding biological function and designing new therapeutics.

Purpose of the Study:

  • To provide a comprehensive overview of experimental phasing techniques as implemented in the SHELX software suite.
  • To guide users through the practical application, challenges, and troubleshooting of experimental phasing.
  • To highlight the integration of experimental phasing with other structure solution methods and automated model building.

Main Methods:

  • Detailed explanation of SHELXC/D/E algorithms, including dual-space direct methods, Patterson seeding, and sphere-of-influence density modification.
  • Description of ANODE for difference map generation and usage in experimental phasing validation.
  • Integration of molecular replacement with experimental phasing strategies.

Main Results:

  • Successful implementation of advanced experimental phasing methods within the SHELX suite.
  • Demonstration of ANODE's utility in validating and aiding experimental phasing.
  • Strategies for overcoming common challenges in substructure searching and density modification.

Conclusions:

  • SHELX provides a robust platform for experimental phasing, offering advanced algorithms and practical solutions.
  • Combining molecular replacement with experimental phasing can enhance structure solution success rates.
  • Automated tools like SHELXE's auto-tracing improve efficiency in the overall structure determination pipeline.