Macromolecular Crystallization and Crystal Perfection

by Chayen, Naomi E; Helliwell, John R; Snell, Edward H

• ISBN13: 9780199213252
• ISBN10: 0199213259
• Format: Hardcover
• Copyright: 2010-05-20
• Publisher: Oxford University Press

Summary

The crystallization of proteins and nucleic acids and/or their complexes has become more highly automated but is still often a trial and error based approach. In parallel, a number of X-ray diffraction based techniques have been developed which explain th

Author Biography

Naomi E. Chayen is Professor of Biomedical Sciences at Imperial College London, Visiting Professor at Harvard Medical School and the President of the International Organisation for Biological Crystallization (IOBCr). She organises and chairs crystallization sessions at international conferences and courses, and is a Crystallization Co-Editor of Acta Crystallographica D.
Professor J.R. Helliwell is Professor of Structural Chemistry at the University of Manchester and an Honorary Visiting Scientist at the STFC Daresbury Laboratory. He has served as Editor-in-Chief of Acta Crystallographica and is currently President of the European Crystallographic Association.
Dr. Edward Snell is Assistant Professor at the Hauptman-Woodward Medical Research Institute at the State University of New York at Buffalo. He has worked at NASA as a senior scientist and was PI on several space missions on the International Space station. He has received a number of academic awards.

Table of Contents

Preface	p. ix
Acknowledgements	p. xi
Introduction and Overview
Introduction	p. 3
Crystal growth	p. 4
Diffraction techniques	p. 6
X-rays	p. 6
Neutrons	p. 7
Crystal volume and quality	p. 9
Short-range order (intermolecular)	p. 10
Long-range order (domain structure)	p. 14
The combination of short- and long-range order	p. 16
Chapter summary	p. 17
Crystallization
Crystallization theory	p. 21
Chapter summary	p. 23
Practical methods of crystallization	p. 24
Batch	p. 24
Vapour diffusion	p. 25
Dialysis	p. 26
Free interface diffusion	p. 26
Converting between methods	p. 27
Chapter summary	p. 28
Screening	p. 29
Screens: problems and new developments	p. 29
Automation-and miniaturization of screening procedures	p. 29
The effect of high-throughput: crystallization robotics	p. 34
Analysis of large quantities of crystallization data	p. 34
Experiment volume considerations	p. 37
Imaging and monitoring of crystallization trials	p. 37
Chapter summary	p. 37
Optimization	p. 38
Practical uses of the crystallization phase diagram	p. 38
Methods for separating nucleation and growth	p. 40
Seeding	p. 41
Dilution techniques	p. 42
The application o flight-scattering techniques	p. 44
Static light scattering	p. 44
Dynamic light scattering	p. 44
Chapter summary	p. 47
Strategies to apply when high-quality crystals cannot be obtained	p. 48
Introduction	p. 48
Non-covalent modification of the sample	p. 48
Covalent modification of the sample	p. 49
Reductive methylation	p. 49
General chemical modification	p. 50
Mutagenesis, domain refinement and homologues	p. 50
Surface-entropy reduction	p. 50
Proteolysis	p. 51
Orthologues and homologues	p. 51
Antibody fragments	p. 52
Chapter summary	p. 52
Membrane proteins	p. 53
Introduction	p. 53
Crystallization	p. 53
Screening with detergents	p. 55
Lipidic cubic-phase crystallization	p. 55
Antibody fragment approaches	p. 56
Characterization using neutron-enhanced contrast	p. 56
Chapter summary	p. 56
Alternative approaches	p. 58
Gel growth	p. 58
Microgravity	p. 59
Interferometry	p. 59
Depletion zone	p. 60
Microfluidics	p. 61
Magnetic and electric fields	p. 62
Chapter summary	p. 64
Diffraction
Experimental aspects	p. 67
The diffraction pattern	p. 67
Structural detail	p. 70
Determining structure when the resolution is not ideal	p. 72
How accurate is the structure?	p. 73
Chapter summary	p. 76
Analysis of the molecular short-range order	p. 78
Structural data	p. 78
Thermal motion and diffuse scattering	p. 79
Diffuse scattering as a source of measurement error in the Bragg intensities	p. 81
Chapter summary	p. 82
Analysis of long-range order	p. 83
Reflection profiling	p. 83
Topography	p. 88
Photography-based topography	p. 89
Digital-based topography	p. 90
Reciprocal-space mapping	p. 91
Combinational analysis and chapter summary	p. 94
Macromolecular crystals and twinning	p. 96
Historical examples	p. 97
Types of twinning	p. 98
The twin fraction and testing for twinned data	p. 102
Using twinned data	p. 104
Overcoming twinning in crystals	p. 105
How prevalent is twinning?	p. 109
Chapter summary	p. 110
Other macromolecular crystal diffraction disorders	p. 112
Introduction	p. 112
Case studies	p. 112
Chapter summary	p. 118
Degradation and improvement of crystal perfection	p. 119
Ageing	p. 119
Radiation damage	p. 119
Cryo-cooling	p. 124
Dehydration and humidity control	p. 127
Chapter summary	p. 131
Unusual diffraction geometries	p. 132
Chapter summary	p. 136
Making the most of difficult crystals - beamline and detector optimization	p. 137
Introduction	p. 137
Geometry and end-station instrumentation	p. 137
Signal and noise considerations	p. 138
Very small crystal volume'microcrystals'	p. 143
Phasing and the available instrumentation	p. 147
Robotics, telepresence and remote access	p. 148
More specialized applications	p. 149
Chapter summary	p. 150
Protein powders-making the most of tiny crystallites in bulk	p. 151
Introduction	p. 151
Quantitative protein powder analyses have opened up in recent years	p. 152
Structure determination of unknown proteins?	p. 154
Characterization of protein crystal polymorphism	p. 155
Chapter summary	p. 156
Complementary techniques	p. 158
Chapter summary	p. 159
The Future
The X-ray laser and the single molecule - no crystal needed?	p. 163
Overall summary and future thoughts	p. 168
Glossary of abbreviations, terms and symbols	p. 170
Abbreviations	p. 170
General	p. 170
Synchrotron sources	p. 171
Neutron sources	p. 171
Terms	p. 171
Crystallization	p. 171
X-ray analysis	p. 172
Symbols	p. 173
Crystallization and crystal-growth-monitoring symbols	p. 173
Diffraction symbols	p. 174
References	p. 175
Index	p. 219
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