# 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 DrenthJeroen 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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