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 |
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