Principles of protein x-ray crystallography / Jan Drenth ; with major contribution from Jeroen Mesters.

Format:

Book

Author/Creator:

Drenth, Jan.

Contributor:

Mesters, Jeroen, 1961-

Hazel M. Hussong Fund.

Language:

English

Subjects (All):

Proteins--Analysis.

Proteins.

X-ray crystallography.

Physical Description:

viii, 332 pages : illustrations ; 25 cm

Edition:

Fourth edition.

Place of Publication:

New York : Springer, 2006.

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).

Contents:

Chapter 1 Crystallizing a Protein 1

1.2 Principles of Protein Crystallization 1

1.3 Crystallization Techniques 4

1.4 Crystallization of Lysozyme 8

1.5 A Preliminary Note on Crystals 9

1.6 Preparation for an X-ray Diffraction Experiment 11

1.7 Cryocooling 15

Chapter 2 X-ray Sources and Detectors 21

2.2 X-ray Sources 21

2.3 Monochromators 30

2.5 Detectors 33

2.6 The Rotation (Oscillation) Instrument 38

Chapter 3 Crystals 45

3.2 Symmetry 49

3.3 Possible Symmetry for Protein Crystals 56

3.4 Coordinate Triplets: General and Special Positions 56

3.5 Asymmetric Unit 57

3.6 Point Groups 58

3.7 Crystal Systems 58

3.8 Radiation Damage 60

3.9 Characterization of the Crystals 61

Chapter 4 Theory of X-ray Diffraction by a Crystal 64

4.2 Waves and Their Addition 65

4.3 A System of Two Electrons 68

4.4 Scattering by an Atom 71

4.5 Scattering by a Unit Cell 73

4.6 Scattering by a Crystal 74

4.7 Diffraction Conditions 76

4.8 Reciprocal Lattice and Ewald Construction 77

4.9 The Temperature Factor 81

4.10 Calculation of the Electron Density (x y z) 84

4.11 Comparison of F(h k l) and F(h k l) 90

4.12 Symmetry in the Diffraction Pattern 91

4.13 Integral Reflection Conditions for Centered Lattices 95

4.14 Intensity Diffracted by a Crystal 96

4.15 Scattering by a Plane of Atoms 103

4.16 Choice of Wavelength, Size of Unit Cell, and Correction of the Diffracted Intensity 105

Chapter 5 Average Reflection Intensity and Distribution of Structure Factor Data 109

5.2 Average Intensity; Wilson Plots 111

5.3 The Distribution of Structure Factors F and Structure Factor Amplitudes |F| 114

5.4 Crystal Twinning 116

Chapter 6 Special Forms of the Structure Factor 119

6.2 The Unitary Structure Factor 119

6.3 The Normalized Structure Factor 120

Chapter 7 The Solution of the Phase Problem by the Isomorphous Replacement Method 123

7.2 The Patterson Function 124

7.3 The Isomorphous Replacement Method 133

7.4 Effect of Heavy Atoms on X-ray Intensities 139

7.5 Determination of the Heavy Atom Parameters from Centrosymmetric Projections 142

7.6 Parameters of Heavy Atoms Derived from Acentric Reflections 144

7.7 The Difference Fourier Summation 146

7.8 Anomalous Scattering 148

7.9 The Anomalous Patterson Summation 152

7.10 One Common Origin for All Derivatives 154

7.11 Refinement of the Heavy Atom Parameters Using Preliminary Protein Phase Angles 157

7.12 Protein Phase Angles 160

7.13 The Remaining Error in the Best Fourier Map 167

7.14 The Single Isomorphous Replacement Method 170

Chapter 8 Phase Improvement 172

8.2 The OMIT Map With and Without Sim Weighting 173

8.3 Solvent Flattening 179

8.4 Noncrystallographic Symmetry and Molecular Averaging 185

8.5 Histogram Matching 187

8.6 wARP: Weighted Averaging of Multiple-Refined Dummy Atomic Models 190

8.7 Further Considerations Concerning Density Modification 192

Chapter 9 Anomalous Scattering in the Determination of the Protein Phase Angles and the Absolute Configuration 194

9.2 Protein Phase Angle Determination with Anomalous Scattering 194

9.3 Improvement of Protein Phase Angles with Anomalous Scattering 196

9.4 The Determination of the Absolute Configuration 198

9.5 Multiple- and Single-Wavelength Anomalous Diffraction (Mad and Sad) 199

Chapter 10 Molecular Replacement 210

10.2 The Rotation Function 211

10.3 The Translation Function 217

Chapter 11 Direct Methods 231

11.2 Shake-and-Bake 231

11.3 SHELXD 236

11.4 The Principle of Maximum Entropy 238

Chapter 12 Laue Diffraction 241

12.2 The Accessible Region of Reciprocal Space 242

12.3 The Multiple Problem 243

12.4 Unscrambling of Multiple Intensities 244

12.5 The Spatial Overlap Problem 245

12.6 Wavelength Normalization 245

Chapter 13 Refinement of the Model Structure 248

13.2 The Mathematics of Refinement 251

13.3 The Principle of the Fast Fourier Transform Method 262

13.4 Specific Refinement Methods 264

Chapter 14 The Combination of Phase Information 279

14.2 Phase Information from Isomorphous Replacement 280

14.3 Phase Information from Anomalous Scattering 282

14.4 Phase Information from Partial Structure Data, Solvent Flattening, and Molecular Averaging 283

14.5 Phase Information from Sad 284

Chapter 15 Checking for Gross Errors and Estimating the Accuracy of the Structural Model 285

15.2 R-Factors 285

15.3 The Ramachandran Plot 287

15.4 Stereochemistry Check 287

15.5 The 3D-1D Profile Method 288

15.6 Quantitative Estimation of the Coordinate Error in the Final Model 292

Chapter 16 Practical Protein Crystallization 297

16.2 Gene Cloning and Expression 298

16.3 Protein Purification 299

16.4 Protein Crystallization 302

Appendix 1 A Compilation of Equations for Calculating Electron Density Maps 305

Appendix 2 A Compilation of Reliability Indexes 308

Appendix 3 The Variation in the Intensity of X-ray Radiation 314.

Notes:

Includes bibliographical references and index.

Local Notes:

Acquired for the Penn Libraries with assistance from the Hazel M. Hussong Fund.

ISBN:

9780387333342

0387333347

OCLC:

81252587