Principles of Protein X-Ray Crystallography by Jan Drenth Third Edition (informative)

Free download Principles of Protein X-Ray Crystallography by Jan Drenth Third Edition
Third Edition
Authors of: Principles of Protein X-Ray Crystallography by Jan Drenth Third Edition
Jan Drenth
Jeroen Mesters
Table of Contents in Principles of Protein X-Ray Crystallography by Jan Drenth Third Edition
Preface to the Third Edition v
Preface to the Second Edition vi
Preface to the First Edition vii
Chapter 1
Crystallizing a Protein
1.1 Introduction
1.2 Principles of Protein Crystallization
1.3 Crystallization Techniques
1.4 Crystallization of Lysozyme
1.5 A Preliminary Note on Crystals
1.6 Preparation for an X-ray Diffraction Experiment
1.7 Cryocooling
1.8 Notes
Summary
Chapter 2
X-ray Sources and Detectors
2.1 Introduction
2.2 X-ray Sources
2.3 Monochromators
2.4 Introduction to Cameras and Detectors
2.5 Detectors
2.6 The Rotation (Oscillation) Instrument
Summary
Chapter 3
Crystals
3.1 Introduction
3.2 Symmetry
3.3 Possible Symmetry for Protein Crystals
3.4 Coordinate Triplets: General and Special Positions
3.5 Asymmetric Unit
3.6 Point Groups
3.7 Crystal Systems
3.8 Radiation Damage
3.9 Characterization of the Crystals
Summary
Chapter 4
Theory of X-ray Diffraction by a Crystal
4.1 Introduction
4.2 Waves and Their Addition
4.3 A System of Two Electrons
4.4 Scattering by an Atom
4.5 Scattering by a Unit Cell
4.6 Scattering by a Crystal
4.7 Diffraction Conditions
4.8 Reciprocal Lattice and Ewald Construction
4.9 The Temperature Factor 81
4.10 Calculation of the Electron Density (xyz)
4.11 Comparison of F(hkl) and F(¯h k¯ ¯l)
4.12 Symmetry in the Diffraction Pattern
4.13 Integral Reflection Conditions for Centered Lattices
4.14 Intensity Diffracted by a Crystal
4.15 Scattering by a Plane of Atoms
4.16 Choice of Wavelength, Size of Unit Cell, and Correction
of the Diffracted Intensity
Summary
Chapter 5
Average Reflection Intensity and Distribution of Structure
Factor Data
5.1 Introduction
5.2 Average Intensity; Wilson Plots
5.3 The Distribution of Structure Factors F and Structure
Factor Amplitudes |F|
5.4 Crystal Twinning
Summary
Chapter 6
Special Forms of the Structure Factor
xii Contents
6.1 Introduction
6.2 The Unitary Structure Factor
6.3 The Normalized Structure Factor
Summary
Chapter 7
The Solution of the Phase Problem by the Isomorphous
Replacement Method
7.1 Introduction
7.2 The Patterson Function
7.3 The Isomorphous Replacement Method
7.4 Effect of Heavy Atoms on X-ray Intensities
7.5 Determination of the Heavy Atom Parameters from
Centrosymmetric Projections
7.6 Parameters of Heavy Atoms Derived from Acentric
Reflections
7.7 The Difference Fourier Summation
7.8 Anomalous Scattering 148
7.9 The Anomalous Patterson Summation
7.10 One Common Origin for All Derivatives
7.11 Refinement of the Heavy Atom Parameters Using
Preliminary Protein Phase Angles
7.12 Protein Phase Angles
7.13 The Remaining Error in the Best Fourier Map
7.14 The Single Isomorphous Replacement Method
Summary
Chapter 8
Phase Improvement
8.1 Introduction
8.2 The OMIT Map With and Without Sim Weighting
8.3 Solvent Flattening
8.4 Noncrystallographic Symmetry and Molecular Averaging
8.5 Histogram Matching
8.6 wARP: Weighted Averaging of Multiple-Refined Dummy
Atomic Models
8.7 Further Considerations Concerning Density Modification
Summary
Chapter 9
Anomalous Scattering in the Determination of the
Protein Phase Angles and the Absolute Configuration
9.1 Introduction
9.2 Protein Phase Angle Determination with Anomalous Scattering
9.3 Improvement of Protein Phase Angles with
Anomalous Scattering
9.4 The Determination of the Absolute Configuration
9.5 Multiple- and Single-Wavelength Anomalous Diffraction
(MAD and SAD)
Chapter
Molecular Replacement
10.1 Introduction
10.2 The Rotation Function
10.3 The Translation Function
Summary
Chapter 11
Direct Methods
11.1 Introduction
11.2 Shake-and-Bake
11.3 SHELXD
11.4 The Principle of Maximum Entropy
Summary
Chapter 12
Laue Diffraction
12.1 Introduction
12.2 The Accessible Region of Reciprocal Space
12.3 The Multiple Problem
12.4 Unscrambling of Multiple Intensities
12.5 The Spatial Overlap Problem
12.6 Wavelength Normalization
Summary
Chapter 13
Refinement of the Model Structure
13.1 Introduction
13.2 The Mathematics of Refinement
13.3 The Principle of the Fast Fourier Transform Method
13.4 Specific Refinement Methods
Summary
Chapter 14
The Combination of Phase Information
14.1 Introduction
14.2 Phase Information from Isomorphous Replacement
14.3 Phase Information from Anomalous Scattering
14.4 Phase Information from Partial Structure Data,
Solvent Flattening, and Molecular Averaging
14.5 Phase Information from SAD
Summary
Chapter 15
Checking for Gross Errors and Estimating the Accuracy
of the Structural Model
15.1 Introduction
15.2 R-Factors
15.3 The Ramachandran Plot
15.4 Stereochemistry Check
15.5 The 3D–1D Profile Method
15.6 Quantitative Estimation of the Coordinate Error in the
Final Model
Summary
Chapter 16
Practical Protein Crystallization
16.1 Introduction
16.2 Gene Cloning and Expression
16.3 Protein Purification
16.4 Protein Crystallization
Summary
Appendix 1
A Compilation of Equations for Calculating Electron
Density Maps
Appendix 2
A Compilation of Reliability Indexes
Appendix 3
The Variation in the Intensity of X-ray Radiation
References
Index
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