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E-grāmata: Introduction to Macromolecular Crystallography

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(University of California at Riverside)
  • Formāts: EPUB+DRM
  • Izdošanas datums: 20-Sep-2011
  • Izdevniecība: Wiley-Blackwell
  • Valoda: eng
  • ISBN-13: 9781118210635
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Introduction to Macromolecular CrystallographyPalielināt
  • Formāts: EPUB+DRM
  • Izdošanas datums: 20-Sep-2011
  • Izdevniecība: Wiley-Blackwell
  • Valoda: eng
  • ISBN-13: 9781118210635
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A comprehensive and approachable introduction to crystallography — now updated in a valuable new edition

The Second Edition of this well-received book continues to offer the most concise, authoritative, and easy-to-follow introduction to the field of crystallography. Dedicated to providing a complete, basic presentation of the subject that does not assume a background in physics or math, the book's content flows logically from basic principles to methods, such as those for solving phase problems, interpretation of Patterson maps and the difference Fourier method, the fundamental theory of diffraction and the properties of crystals, and applications in determining macromolecular structure.

This new edition includes a vast amount of carefully updated materials, as well as two completely new chapters on recording and compiling X-ray data and growing crystals of proteins and other macromolecules.

Richly illustrated throughout to clarify difficult concepts, this book takes a non-technical approach to crystallography that is ideal for professionals and graduate students in structural biology, biophysics, biochemistry, and molecular biology who are studying the subject for the first time.

PREFACE ix
1 AN OVERVIEW OF MACROMOLECULAR CRYSTALLOGRAPHY 1
What Do We Mean by the Structure of Something?
1
An Analogy
2
A Lens and Optical Diffraction Patterns
6
How X-Ray Diffraction Works
11
The Phase Problem
15
The Electron Density
16
2 CRYSTALLIZATION OF MACROMOLECULES 19
Crystals Grow from Supersaturated Solutions
20
Why Crystals Grow
22
Proteins Present Special Problems for Crystallographers
23
Properties of Macromolecular Crystals
23
Crystallization Strategy
24
Screening and Optimization
28
Creating the Supersaturated State
29
Precipitating Agents
35
Factors Influencing Protein Crystal Growth
39
Some Useful Considerations
40
Typical Trial Arrays
42
The Importance of Protein Purity and Homogeneity
43
Solubilization
44
Seeding
45
Automated Crystallization and Robotics
47
Important Principles
49
3 THE NATURE OF CRYSTALS: SYMMETRY AND THE UNIT CELL 50
The Asymmetric Unit
50
The Space Group
51
The Unit Cell
53
The Lattice Translations
57
Symmetry and Equivalent Positions
60
Why So Few Kinds of Unit Cells
63
Primitive and Centered Lattices
64
Planes, Miller Indexes, and Convolutions
66
The Reciprocal Lattice
71
Crystals as Waves of Electrons in Three-Dimensional Space
73
4 WAVES AND THEIR PROPERTIES 77
The Properties of Waves
77
Waves as Vectors and Complex Numbers
79
Addition of Waves
81
Manipulating Vectors
85
Some Useful Wave Relationships
85
The Fourier Synthesis, Planes, and the Electron Density
88
5 DIFFRACTION FROM POINTS, PLANES, MOLECULES, AND CRYSTALS 93
Diffraction Pattern of an Arbitrary Array of Points in Space
94
Diffraction from Equally Spaced Points Along a Line
98
Diffraction from a Plane, Families of Planes, and Lattices of Points
100
Continuous and Discontinuous Transforms
103
Diffraction from a Crystal
107
The Structure Factor for a Crystal
110
The Structure Factor as a Product of Transforms
114
Temperature Factors
116
Centers of Symmetry
117
Friedel's Law
118
Anomalous Dispersion Effects
119
The Electron Density Equation
120
The Phase Problem
123
6 INTERPRETATION OF DIFFRACTION PATTERNS 125
Diffraction Patterns, Planes, and Reciprocal Space
125
Ewald's Sphere
126
Crystal Symmetry and the Symmetry of the Diffraction Pattern
130
Symmetry and Systematic Absences
131
Analysis of Diffraction Patterns
134
Symmetry in Diffraction Space
141
More Thoughts on Space Groups
145
Other Information in Diffraction Patterns
147
7 DATA COLLECTION 150
What is Involved
150
X-ray Sources and the Production of X Rays
151
Detectors and the Recording of Diffraction Intensities
155
Data Management Procedures
159
Crystal Mounting and Handling
159
X-ray Data Processing
161
Scaling of X-ray Diffraction Data
164
Real Space and Diffraction Space
167
8 SOLVING THE PHASE PROBLEM 170
Patterson Methods
171
The Heavy Atom Method
171
The R Factor and Crystallographic Refinement
173
Isomorphous Replacement
174
Formulation of Isomorphous Replacement in Protein Crystallography
179
Isomorphous Replacement in Practice
181
Molecular Replacement
183
Phase Extension Using Noncrystallographic Symmetry
187
Anomalous Scattering Approaches
188
Direct Methods
191
9 INTERPRETING PATTERSON MAPS 193
What Is a Patterson Map
194
Creating a Patterson Map From a Crystal
197
Patterson Maps as Molecular Covolutions
200
Deconvoluting Patterson Maps
200
Harker Planes or Sections
201
Using the Patterson Map for Isomorphous Replacement
207
10 ELECTRON DENSITY, REFINEMENT, AND DIFFERENCE FOURIER MAPS 211
Resolution of Electron Density Maps
213
Interpretation of Electron Density Maps
216
Constructing a Model
217
Model Refinement
220
Reciprocal Space Refinement: Least Squares
221
Real Space Refinement: Difference Fourier Syntheses
224
Additional Considerations in Refinement
226
The Free R Factor
228
Some General Observations
229
Criteria for Judging a Structure Determination
229
Biochemical Experiments Using X-ray Crystallography
232
The Difference Fourier Method
233
BIBLIOGRAPHY 238
INDEX 243
Alexander Mcpherson, PhD, is Professor in the Department of Molecular Biology and Biochemistry at the University of California, Irvine's School of Biological Sciences. The author of six books and 300 papers or reviews, he is widely considered the nation's foremost authority in the field of macromolecular crystallography. For over a decade, he has served as principal instructor of the Cold Spring Harbor Laboratory course inmacromolecular X-ray crystallography, an intensive course for which much of the material in this text was originally conceived.
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