Practical Protein Crystallography (eBook)

Front Cover 1
Practical Protein Crystallography 4
Copyright Page 5
Contents 6
Foreword To The Second Edition 14
Preface To The Second Edition 16
Acknowledgments 20
Chapter 1. LABORATORY TECHNIQUES 22
1.1 Preparing Protein Samples 22
1.2 Protein Crystal Growth 27
1.3 Crystal Storage and Handling 38
1.4 Crystal Soaking 39
1.5 Anaerobic Crystals 41
Chapter 2. DATA COLLECTION TECHNIQUES 44
2.1 Preparing Crystals for Data Collection 44
2.2 Optical Alignment 52
2.3 X-Ray Sources 55
2.4 Preliminary Characterization 60
2.5 Heavy-Atom Derivative Scanning with Film 85
2.6 Overall Data Collection Strategy 88
2.7 Overview of Older Film Techniques 94
2.8 Four-Circle Diffractometer Data Collection 95
2.9 Area Detector Data Collection 97
2.10 Image Plate Data Collection 103
2.11 Synchrotron Radiation Light Sources 105
2.12 Data Reduction 108
Chapter 3. COMPUTATIONAL TECHNIQUES 112
3.1 Terminology 114
3.2 Basic Computer Techniques 123
3.3 Data Reduction and Statistical Analysis 136
3.4 The Patterson Synthesis 145
3.5 Fourier Techniques 158
3.6 Isomorphous Replacement Phasing 166
3.7 Molecular Replacement 183
3.8 Noncrystallographic Symmetry 192
3.9 Density Modification 197
3.10 Multiwavelength Data with Anomalous Scattering 203
3.11 Refinement of Coordinates 214
3.12 Fitting of Maps 238
3.13 Analysis of Coordinates 286
Chapter 4. XtalView TUTORIALS 292
4.1 Installation 292
4.2 Obtaining Help 293
4.3 Xview 293
4.4 A Typical Manual Fitting Session with Xfit 324
4.5 Interfacing to Other Programs 347
Chapter 5. PROTEIN CRYSTALLOGRAPHY COOKBOOK 350
5.1 Multiple Isomorphous Replacement 350
5.2 Mutant Studies 387
5.3 Substrate-Analog Example 401
5.4 Molecular Replacement 405
5.5 Multiwavelength Anomalous Dispersion (MAD) Phasing 409
Chapter 6. CRYOCRYSTALLOGRAPHY: BASIC THEORY AND METHODS 430
6.1 Overview 431
6.2 Theory 432
6.3 Room Temperature versus Low-Temperature Crystallography 434
6.4 Cryogenic Safety 436
6.5 Equipment 437
6.6 Crystal Loop Mounting Techniques 444
6.7 Crystal Storage Overview 448
6.8 Crystal Removal and Storage 453
6.9 Crystal Handling 462
APPENDIX A: Crystallographic Equations in Computer Code 466
APPENDIX B: Useful Web Sites 476
Practical Protein Crystallography II Web Site 476
Software Web Sites 476
Databases 480
Synchrotrons 480
Useful Information 481
Heavy-Atom Information 481
Crystallization 482
X-Ray Anomalous Scattering 482
X-Ray Equipment Vendors 482
Crystallographic Associations 482
Index 484
Color Plates Section 500