Outline of crystallography for biologists PDF
Preview Outline of crystallography for biologists
Outline of Crystallography for Biologists Outline of Crystallography for Biologists David Blow Senior Research Fellow Imperial College of Science, Technology and Medicine 1 1 Great Clarendon Street, Oxford OX2 6DP Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide in Oxford New York Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto With offices in Argentina Austria Brazil Chile Czech Republic France Greece Guatemala Hungary Italy Japan South Korea Poland Portugal Singapore Switzerland Thailand Turkey Ukraine Vietnam Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries Published in the United States by Oxford University Press Inc., New York © Oxford University Press 2002 The moral rights of the author have been asserted Database right Oxford University Press (maker) Reprinted 2003 (with corrections), 2004 (with corrections), 2010 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this book in any other binding or cover And you must impose this same condition on any acquirer ISBN978-0-19-851051-2 Printed in the United Kingdom by Lightning Source UK Ltd., Milton Keynes Contents Preface vii Introductory note ix Part 1 Fundamentals 1 1 Images and X-rays 3 2 Crystals and symmetry 22 3 Waves 45 4 Diffraction 57 5 Diffraction by crystals 82 Part 2 Practice 103 6 Intensity measurements 105 7 Isomorphous replacement 121 8 Anomalous scattering 147 9 Molecular replacement 162 10 Density-modification procedures: improving a calculated map before interpretation 177 11 Electron-density maps 191 12 Structural refinement 205 13 Accuracy of the final model 222 References 229 Index 233 Preface I dedicate this book to Max Perutz, who built on Desmond Bernal’s vision and Dorothy Hodgkin’s determination, and created a practical method for visualizing macromolecular structure. He was my guiding (but never direct- ing) PhD supervisor. Later he became the inspirational head of the hugely successful Laboratory of Molecular Biology in Cambridge. He called him- self its Chairman, never the Director. It was a privilege to have worked under him and with him. Fifty years ago macromolecular structure analysis had never been done, and many thought it impossible. Now it is a daily routine, and the book owes most to those whose crucial contributions have brought this about. I make no attempt to separate the key discoveries that represent the many steps that led along the road, and to identify ‘who did what’. I believe my colleagues who have pioneered those discoveries will understand why. The book would have been littered with references, it would have been neces- sary to refer to details and difficulties which now seem insignificant, and some questions of originality and priority might have been hard to resolve. Such details would be inappropriate in this book which is intended to be no more than a simple outline of the subject. I owe a debt of gratitude to those who have helped with this publication. They have generously allowed me to mention their work and to use their illustrations, often going to great lengths to provide high-quality figures. Many have read chapters, and commented helpfully on my drafts. To illus- trate points that are rarely published in detail, I have had to take examples from doctoral theses, and I am particularly grateful to my former students, and others, who have allowed me to use their earliest research work in this way. Special acknowledgment is due to two professional artists, who have cre- ated a few beautiful drawings for me—Neil Powell and Gerard Lindley. Another special notice is due to Ken Holmes, co-author of a review we wrote together in 1965, and which is, in some senses, the parent of this vol- ume, and to his wife Mary who drew the original duck. Rachel Leveridge drew the duck which appears repeatedly in this volume. I must take respon- sibility for the less artistic figures. I am grateful to all these helpers, many of them good friends, but includ- ing some whom I have never met. A few of them are named below. VIII PREFACE Alan Wonacott Guy Pallardy Naoki Kinushima Alexy Teplyakov Helen Price Neil Powell Alice Vrielink Ian Johnston Nobutoshi Ito Alwyn Jones Irene Gonsalvez Peter Brick Amanda Brindley Jean-René Regnard Peter Main Andy Leslie Jenny Littlechild Rachel Leveridge Anne Bloomer Jim Raftery Richard Bytheway (Bede Axel Brünger John Helliwell Scientific) Bram Schierbeek (Nonius) John Squire Richard Wellberry Charles Taylor Jonathan Goldberg Silvia Onesti Chris Hammond Katy Brown Simon Phillips Christine Muchmore (Mar) Keith Watenpaugh Stephen Bragg Daniel Schlieper Kosuke Morikawa Stephen Lee David Rice Linda Britton Steve Harrison Don Caspar Lingling Chen Steve Lipson Edward Hollingsworth Lyle Jensen Uli Arndt Eleanor Dodson Marie-Claude Moissenet V. Ramakrishnan Elspeth Garman Max Perutz Wayne Hendrickson Emmanuel Saridakis Micha Isupov Wolfram Saenger Frank James Michael Rossmanm Gerard Lindley Michael Woolfson David Blow Appledore, Devon October 2001
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