Crystallography Made Crystal Clear - A Guide for Users of Macromolecular Models 2nd ed - G. Rhodes (AP, 2000) WW.pdf

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TITLE
Crystallograph
Mad
Crystal Clear:
Model
Second Edjtion
Gale Rhodes
Department of Chemistry
University of Southern Maine
Portland, Maine
CMCC Home Page: www. usm.maine.edu/-rhodes/CMCC
ACADEMIC PRESS
San Diego San Francisco New York Boston London Sydney Tokyo
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This book is printed on acid-free paper. @
Copyright 02000, 1993 Elsevier Science (USA).
All Rights Reserved.
No part of this publication may be reproduced or transmitted in any form or by any
means, electronic or mechanical, including photocopy, recording, or any information
storage and retrieval system, without permission in writing from the publisher.
Requests for permission to make copies of any part of the work should be mailed to:
Permissions Department, Academic Press, 6277 Sea Harbor Drive,
Orlando, Florida 32887-6777
Academic Press
An imprint of Elsevier Science
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http:Nwww.academicpress.com
Academic Press
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Library of Congress Catalog Card Number: 99-63088
International Standard Book Number: 0-12-587072-8
PRINTED IN THE UNITED STATES OF AMERICA
03 04 05 06 07
9876543
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Like everything, for Pam.
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Contents
Preface to the Second Edition
xm
...
Preface to the First Edition
xvii
1. Model and Molecule
I
2. An Overview of Protein Crystallography
I. Introduction 5
A. Obtaining an image of a microscopic object
B. Obtaining images of molecules 7
C. A thumbnail sketch of protein crystallography
11. Crystals 8
A. The nature of crystals
8
B. Growing crystals
9
III. Collecting X-ray data
10
IV. Diffraction 12
A. Simple objects 12
B. Arrays of simple objects: Real and reciprocal lattices
13
C. Intensities of reflections 14
D. Arrays of complex objects 15
E. Thee-dimensional arrays 16
V. Coordinate systems in crystallography 17
VI. The mathematics of crystallography: A brief description
19
A. Wave equations: Periodic functions 19
B . Complicated periodic functions: Fourier series
20
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U. Electron-density maps 24
E. Electron density from structure factors
25
F. Electron density from measured reflections
27
G. Obtaining a model
28
3. Protein Crystals
29
I. Properties of protein crystals
29
A. Introduction 29
B. Size, structural integrity, and mosaicity
29
C. Multiple crystalline forms
3 1
D.Watercontent 32
11. Evidence that solution and crystal structures are similar
33
A. Proteins retain their function in the crystal 33
B. X-ray structures are compatible with other structural
evidence 34
C. Other evidence 34
III. Growing protein crystals
35
A. Introduction 35
B. Growing crystals: Basic procedure
35
C. Growing derivative crystals 37
D. Finding optimal conditions for crystal growth
37
IV. Judging crystal quality 41
V. Mounting crystals for data collection
43
4. Collecting Diffraction Data
45
I. Introduction 45
11. Geometric principles of diffraction
45
A. The generalized unit cell 46
B. Indices of the atomic planes in a crystal 47
C. Conditions that produce diffraction: Bragg's law
50
D. The reciprocal lattice 52
E. Bragg 7 s law in reciprocal space 55
F. The number of measurable reflections
58
G. Unit-cell dimensions 60
H. Unit-cell symmetry 60
III. Collecting X-ray difYraction data
64
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