Principles of Protein X-Ray Crystallography,9780387333342

Principles of Protein X-Ray Crystallography

by ;
Edition: 3rd
ISBN13: 9780387333342
ISBN10: 0387333347
Format: Hardcover
Pub. Date: 2006-11-10
Publisher(s): Springer Nature
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Summary

X-ray crystallography has long been a vital method for studying the structure of proteins and other macromolecules. As the importance of proteins continues to grow, in fields from biochemistry and biophysics to pharmaceutical development and biotechnology, many researchers have found that a knowledge of X-ray diffraction is an indispensable tool. In this new edition of his essential work, Dr. Jan Drenth, recognized internationally for his numerous contributions to crystallographic research, has provided an up-to-date and technically rigorous introduction to the subject. Principles of Protein X-ray Crystallography provides the theoretical background necessary to understand how the structure of proteins is determined at atomic resolution. It is intended to serve as an introduction for graduate students, postdoctoral researchers, and established scientists who want to use protein crystallography in their own endeavors, or need to understand the subject in order to critically evaluate the literature. New additions to the book include a section on twinning, an additional chapter on crystal growth and a discussion of single-wavelength anomalous dispersion (SAD). About the Authors: Dr. Jan Drenth is a professor emeritus at the Laboratory of Biophysical Chemistry at the University of Groningen, The Netherlands. Contributing author Dr. Jeroen R. Mesters Ph.D. is a Senior Research Assistant at the Institute of Biochemistry, University of Luebeck, Germany.

Author Biography

Dr. Jan Drenth is a professor emeritus at the Laboratory of Biophysical Chemistry at the University of Groningen, The Netherlands.Contributing author Dr. Jeroen R. Mesters Ph.D. is a Senior Research Assistant at the Institute of Biochemistry, University of Luebeck, Germany.

Table of Contents

Preface to the Third Edition v
Preface to the Second Edition vi
Preface to the First Edition vii
Chapter 1 Crystallizing a Protein 1(20)
1.1 Introduction
1(1)
1.2 Principles of Protein Crystallization
1(3)
1.3 Crystallization Techniques
4(4)
1.4 Crystallization of Lysozyme
8(1)
1.5 A Preliminary Note on Crystals
9(2)
1.6 Preparation for an X-ray Diffraction Experiment
11(4)
1.7 Cryocooling
15(2)
1.8 Notes
17(3)
Summary
20(1)
Chapter 2 X-ray Sources and Detectors 21(24)
2.1 Introduction
21(1)
2.2 X-ray Sources
21(9)
2.3 Monochromators
30(1)
2.4 Introduction to Cameras and Detectors
31(2)
2.5 Detectors
33(5)
2.6 The Rotation (Oscillation) Instrument
38(5)
Summary
43(2)
Chapter 3 Crystals 45(19)
3.1 Introduction
45(4)
3.2 Symmetry
49(7)
3.3 Possible Symmetry for Protein Crystals
56(1)
3.4 Coordinate Triplets: General and Special Positions
56(1)
3.5 Asymmetric Unit
57(1)
3.6 Point Groups
58(1)
3.7 Crystal Systems
58(2)
3.8 Radiation Damage
60(1)
3.9 Characterization of the Crystals
61(2)
Summary
63(1)
Chapter 4 Theory of X-ray Diffraction by a Crystal 64(45)
4.1 Introduction
64(1)
4.2 Waves and Their Addition
65(3)
4.3 A System of Two Electrons
68(3)
4.4 Scattering by an Atom
71(2)
4.5 Scattering by a Unit Cell
73(1)
4.6 Scattering by a Crystal
74(2)
4.7 Diffraction Conditions
76(1)
4.8 Reciprocal Lattice and Ewald Construction
77(4)
4.9 The Temperature Factor
81(3)
4.10 Calculation of the Electron Density p(x y z)
84(6)
4.11 Comparison of F(h k 1) and F(h k l)
90(1)
4.12 Symmetry in the Diffraction Pattern
91(4)
4.13 Integral Reflection Conditions for Centered Lattices
95(1)
4.14 Intensity Diffracted by a Crystal
96(7)
4.15 Scattering by a Plane of Atoms
103(2)
4.16 Choice of Wavelength, Size of Unit Cell, and Correction of the Diffracted Intensity
105(2)
Summary
107(2)
Chapter 5 Average Reflection Intensity and Distribution of Structure Factor Data 109(10)
5.1 Introduction
109(2)
5.2 Average Intensity; Wilson Plots
111(3)
5.3 The Distribution of Structure Factors F and Structure Factor Amplitudes |F|
114(2)
5.4 Crystal Twinning
116(2)
Summary
118(1)
Chapter 6 Special Forms of the Structure Factor 119(4)
6.1 Introduction
119(1)
6.2 The Unitary Structure Factor
119(1)
6.3 The Normalized Structure Factor
120(2)
Summary
122(1)
Chapter 7 The Solution of the Phase Problem by the Isomorphous Replacement Method 123(49)
7.1 Introduction
123(1)
7.2 The Patterson Function
124(9)
7.3 The Isomorphous Replacement Method
133(6)
7.4 Effect of Heavy Atoms on X-ray Intensities
139(3)
7.5 Determination of the Heavy Atom Parameters from Centrosymmetric Projections
142(2)
7.6 Parameters of Heavy Atoms Derived from Acentric Reflections
144(2)
7.7 The Difference Fourier Summation
146(2)
7.8 Anomalous Scattering
148(4)
7.9 The Anomalous Patterson Summation
152(2)
7.10 One Common Origin for All Derivatives
154(3)
7.11 Refinement of the Heavy Atom Parameters Using Preliminary Protein Phase Angles
157(3)
7.12 Protein Phase Angles
160(7)
7.13 The Remaining Error in the Best Fourier Map
167(3)
7.14 The Single Isomorphous Replacement Method
170(1)
Summary
171(1)
Chapter 8 Phase Improvement 172(22)
8.1 Introduction
172(1)
8.2 The OMIT Map With and Without Sim Weighting
173(6)
8.3 Solvent Flattening
179(6)
8.4 Noncrystallographic Symmetry and Molecular Averaging
185(2)
8.5 Histogram Matching
187(3)
8.6 wARP: Weighted Averaging of Multiple-Refined Dummy Atomic Models
190(2)
8.7 Further Considerations Concerning Density Modification
192(1)
Summary
193(1)
Chapter 9 Anomalous Scattering in the Determination of the Protein Phase Angles and the Absolute Configuration 194(16)
9.1 Introduction
194(1)
9.2 Protein Phase Angle Determination with Anomalous Scattering
194(2)
9.3 Improvement of Protein Phase Angles with Anomalous Scattering
196(2)
9.4 The Determination of the Absolute Configuration
198(1)
9.5 Multiple- and Single-Wavelength Anomalous Diffraction (MAD and SAD)
199(10)
Summary
209(1)
Chapter 10 Molecular Replacement 210(21)
10.1 Introduction
210(1)
10.2 The Rotation Function
211(6)
10.3 The Translation Function
217(13)
Summary
230(1)
Chapter 11 Direct Methods 231(10)
11.1 Introduction
231(1)
11.2 Shake-and-Bake
231(5)
11.3 SHELXD
236(2)
11.4 The Principle of Maximum Entropy
238(2)
Summary
240(1)
Chapter 12 Laue Diffraction 241(7)
12.1 Introduction
241(1)
12.2 The Accessible Region of Reciprocal Space
242(1)
12.3 The Multiple Problem
243(1)
12.4 Unscrambling of Multiple Intensities
244(1)
12.5 The Spatial Overlap Problem
245(1)
12.6 Wavelength Normalization
245(1)
Summary
246(2)
Chapter 13 Refinement of the Model Structure 248(31)
13.1 Introduction
248(3)
13.2 The Mathematics of Refinement
251(11)
13.3 The Principle of the Fast Fourier Transform Method
262(2)
13.4 Specific Refinement Methods
264(14)
Summary
278(1)
Chapter 14 The Combination of Phase Information 279(6)
14.1 Introduction
279(1)
14.2 Phase Information from Isomorphous Replacement
280(2)
14.3 Phase Information from Anomalous Scattering
282(1)
14.4 Phase Information from Partial Structure Data, Solvent Flattening, and Molecular Averaging
283(1)
14.5 Phase Information from SAD
284(1)
Summary
284(1)
Chapter 15 Checking for Gross Errors and Estimating the Accuracy of the Structural Model 285(12)
15.1 Introduction
285(1)
15.2 R-Factors
285(2)
15.3 The Ramachandran Plot
287(1)
15.4 Stereochemistry Check
287(1)
15.5 The 3D-1D Profile Method
288(4)
15.6 Quantitative Estimation of the Coordinate Error in the Final Model
292(4)
Summary
296(1)
Chapter 16 Practical Protein Crystallization 297(8)
16.1 Introduction
297(1)
16.2 Gene Cloning and Expression
298(1)
16.3 Protein Purification
299(3)
16.4 Protein Crystallization
302(1)
Summary
303(2)
Appendix 1 A Compilation of Equations for Calculating Electron Density Maps 305(3)
Appendix 2 A Compilation of Reliability Indexes 308(6)
Appendix 3 The Variation in the Intensity of X-ray Radiation 314(2)
References 316(10)
Index 326

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