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Protein Crystallography

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Cover of 'Protein Crystallography'

Table of Contents

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    Book Overview
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    Chapter 1 Expression and Purification of Recombinant Proteins in Escherichia coli with a His6 or Dual His6-MBP Tag
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    Chapter 2 Protein Crystallization
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    Chapter 3 Advanced Methods of Protein Crystallization
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    Chapter 4 The “Sticky Patch” Model of Crystallization and Modification of Proteins for Enhanced Crystallizability
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    Chapter 5 Crystallization of Membrane Proteins: An Overview
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    Chapter 6 Locating and Visualizing Crystals for X-Ray Diffraction Experiments
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    Chapter 7 Collection of X-Ray Diffraction Data from Macromolecular Crystals
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    Chapter 8 Identifying and Overcoming Crystal Pathologies: Disorder and Twinning
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    Chapter 9 Applications of X-Ray Micro-Beam for Data Collection
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    Chapter 10 Serial Synchrotron X-Ray Crystallography (SSX)
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    Chapter 11 Time-Resolved Macromolecular Crystallography at Modern X-Ray Sources
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    Chapter 12 Structure Determination Using X-Ray Free-Electron Laser Pulses
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    Chapter 13 Processing of XFEL Data
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    Chapter 14 Many Ways to Derivatize Macromolecules and Their Crystals for Phasing
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    Chapter 15 Experimental Phasing: Substructure Solution and Density Modification as Implemented in SHELX
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    Chapter 16 Contemporary Use of Anomalous Diffraction in Biomolecular Structure Analysis
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    Chapter 17 Long-Wavelength X-Ray Diffraction and Its Applications in Macromolecular Crystallography
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    Chapter 18 Acknowledging Errors: Advanced Molecular Replacement with Phaser
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    Chapter 19 Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems
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    Chapter 20 Radiation Damage in Macromolecular Crystallography
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    Chapter 21 Boxes of Model Building and Visualization
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    Chapter 22 Structure Refinement at Atomic Resolution
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    Chapter 23 Low Resolution Refinement of Atomic Models Against Crystallographic Data
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    Chapter 24 Stereochemistry and Validation of Macromolecular Structures
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    Chapter 25 Validation of Protein–Ligand Crystal Structure Models: Small Molecule and Peptide Ligands
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    Chapter 26 Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive
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    Chapter 27 Databases, Repositories, and Other Data Resources in Structural Biology
Attention for Chapter 18: Acknowledging Errors: Advanced Molecular Replacement with Phaser
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Chapter title
Acknowledging Errors: Advanced Molecular Replacement with Phaser
Chapter number 18
Book title
Protein Crystallography
Published in
Methods in molecular biology, June 2017
DOI 10.1007/978-1-4939-7000-1_18
Pubmed ID
Book ISBNs
978-1-4939-6998-2, 978-1-4939-7000-1
Authors

Airlie J. McCoy

Editors

Alexander Wlodawer, Zbigniew Dauter, Mariusz Jaskolski

Abstract

Molecular replacement is a method for solving the crystallographic phase problem using an atomic model for the target structure. State-of-the-art methods have moved the field significantly from when it was first envisaged as a method for solving cases of high homology and completeness between a model and target structure. Improvements brought about by application of maximum likelihood statistics mean that various errors in the model and pathologies in the data can be accounted for, so that cases hitherto thought to be intractable are standardly solvable. As a result, molecular replacement phasing now accounts for the lion's share of structures deposited in the Protein Data Bank. However, there will always be cases at the fringes of solvability. I discuss here the approaches that will help tackle challenging molecular replacement cases.

Mendeley readers

The data shown below were compiled from readership statistics for 15 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 15 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 4 27%
Student > Ph. D. Student 3 20%
Student > Bachelor 2 13%
Lecturer 1 7%
Student > Master 1 7%
Other 1 7%
Unknown 3 20%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 4 27%
Chemistry 3 20%
Pharmacology, Toxicology and Pharmaceutical Science 1 7%
Agricultural and Biological Sciences 1 7%
Unspecified 1 7%
Other 0 0%
Unknown 5 33%