Principles of Protein X-Ray Crystallography

By: Jan Drenth

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Hardcover | 9 November 2006 | Edition Number 3

At a Glance

Hardcover
332 Pages

Edition Type
Revised

Dimensions(cm)
23.5 x 15.5 x 2.06

Hardcover

$186.41

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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.

Industry Reviews

From the reviews of the third edition:

"This book, Principles of Protein X-ray Crystallography, aims to satisfy nearly everyone; ... The volume is well organized ... . this is a solid book by an experienced protein crystallographer. It covers the full spectrum of subjects for a professional structural biologist. Specialized subjects are kept in separate chapters so the book can be parsed by those interested in the big picture of the method. ... it is probably the most definitive work that is currently available for structural biologists." (Jon Robertus, Journal of the American Chemical Society, Vol. 129 (17), 2007)

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Preface to the Third Edition	p. v
Preface to the Second Edition	p. vi
Preface to the First Edition	p. vii
Crystallizing a Protein	p. 1
Introduction	p. 1
Principles of Protein Crystallization	p. 1
Crystallization Techniques	p. 4
Crystallization of Lysozyme	p. 8
A Preliminary Note on Crystals	p. 9
Preparation for an X-ray Diffraction Experiment	p. 11
Cryocooling	p. 15
Notes	p. 17
Summary	p. 20
X-ray Sources and Detectors	p. 21
Introduction	p. 21
X-ray Sources	p. 21
Monochromators	p. 30
Introduction to Cameras and Detectors	p. 31
Detectors	p. 33
The Rotation (Oscillation) Instrument	p. 38
Summary	p. 43
Crystals	p. 45
Introduction	p. 45
Symmetry	p. 49
Possible Symmetry for Protein Crystals	p. 56
Coordinate Triplets: General and Special Positions	p. 56
Asymmetric Unit	p. 57
Point Groups	p. 58
Crystal Systems	p. 58
Radiation Damage	p. 60
Characterization of the Crystals	p. 61
Summary	p. 63
Theory of X-ray Diffraction by a Crystal	p. 64
Introduction	p. 64
Waves and Their Addition	p. 65
A System of Two Electrons	p. 68
Scattering by an Atom	p. 71
Scattering by a Unit Cell	p. 73
Scattering by a Crystal	p. 74
Diffraction Conditions	p. 76
Reciprocal Lattice and Ewald Construction	p. 77
The Temperature Factor	p. 81
Calculation of the Electron Density (x y z)	p. 84
Comparison of F(h k l) and F(h k l)	p. 90
Symmetry in the Diffraction Pattern	p. 91
Integral Reflection Conditions for Centered Lattices	p. 95
Intensity Diffracted by a Crystal	p. 96
Scattering by a Plane of Atoms	p. 103
Choice of Wavelength, Size of Unit Cell, and Correction of the Diffracted Intensity	p. 105
Summary	p. 107
Average Reflection Intensity and Distribution of Structure Factor Data	p. 109
Introduction	p. 109
Average Intensity; Wilson Plots	p. 111
The Distribution of Structure Factors F and Structure Factor Amplitudes F	p. 114
Crystal Twinning	p. 116
Summary	p. 118
Special Forms of the Structure Factor	p. 119
Introduction	p. 119
The Unitary Structure Factor	p. 119
The Normalized Structure Factor	p. 120
Summary	p. 122
The Solution of the Phase Problem by the Isomorphous Replacement Method	p. 123
Introduction	p. 123
The Patterson Function	p. 124
The Isomorphous Replacement Method	p. 133
Effect of Heavy Atoms on X-ray Intensities	p. 139
Determination of the Heavy Atom Parameters from Centrosymmetric Projections	p. 142
Parameters of Heavy Atoms Derived from Acentric Reflections	p. 144
The Difference Fourier Summation	p. 146
Anomalous Scattering	p. 148
The Anomalous Patterson Summation	p. 152
One Common Origin for All Derivatives	p. 154
Refinement of the Heavy Atom Parameters Using Preliminary Protein Phase Angles	p. 157
Protein Phase Angles	p. 160
The Remaining Error in the Best Fourier Map	p. 167
The Single Isomorphous Replacement Method	p. 170
Summary	p. 171
Phase Improvement	p. 172
Introduction	p. 172
The OMIT Map With and Without Sim Weighting	p. 173
Solvent Flattening	p. 179
Noncrystallographic Symmetry and Molecular Averaging	p. 185
Histogram Matching	p. 187
wARP: Weighted Averaging of Multiple-Refined Dummy Atomic Models	p. 190
Further Considerations Concerning Density Modification	p. 192
Summary	p. 193
Anomalous Scattering in the Determination of the Protein Phase Angles and the Absolute Configuration	p. 194
Introduction	p. 194
Protein Phase Angle Determination with Anomalous Scattering	p. 194
Improvement of Protein Phase Angles with Anomalous Scattering	p. 196
The Determination of the Absolute Configuration	p. 198
Multiple- and Single-Wavelength Anomalous Diffraction (Mad and Sad)	p. 199
Summary	p. 209
Molecular Replacement	p. 210
Introduction	p. 210
The Rotation Function	p. 211
The Translation Function	p. 217
Summary	p. 230
Direct Methods	p. 231
Introduction	p. 231
Shake-and-Bake	p. 231
SHELXD	p. 236
The Principle of Maximum Entropy	p. 238
Summary	p. 240
Laue Diffraction	p. 241
Introduction	p. 241
The Accessible Region of Reciprocal Space	p. 242
The Multiple Problem	p. 243
Unscrambling of Multiple Intensities	p. 244
The Spatial Overlap Problem	p. 245
Wavelength Normalization	p. 245
Summary	p. 246
Refinement of the Model Structure	p. 248
Introduction	p. 248
The Mathematics of Refinement	p. 251
The Principle of the Fast Fourier Transform Method	p. 262
Specific Refinement Methods	p. 264
Summary	p. 278
The Combination of Phase Information	p. 279
Introduction	p. 279
Phase Information from Isomorphous Replacement	p. 280
Phase Information from Anomalous Scattering	p. 282
Phase Information from Partial Structure Data, Solvent Flattening, and Molecular Averaging	p. 283
Phase Information from Sad	p. 284
Summary	p. 284
Checking for Gross Errors and Estimating the Accuracy of the Structural Model	p. 285
Introduction	p. 285
R-Factors	p. 285
The Ramachandran Plot	p. 287
Stereochemistry Check	p. 287
The 3D-1D Profile Method	p. 288
Quantitative Estimation of the Coordinate Error in the Final Model	p. 292
Summary	p. 296
Practical Protein Crystallization	p. 297
Introduction	p. 297
Gene Cloning and Expression	p. 298
Protein Purification	p. 299
Protein Crystallization	p. 302
Summary	p. 303
A Compilation of Equations for Calculating Electron Density Maps	p. 305
A Compilation of Reliability Indexes	p. 308
The Variation in the Intensity of X-ray Radiation	p. 314
References	p. 316
Index	p. 326
Table of Contents provided by Ingram. All Rights Reserved.

Principles of Protein X-Ray Crystallography

At a Glance

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Industry Reviews

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