9780125870733

Crystallography Made Crystal Clear

by
  • ISBN13:

    9780125870733

  • ISBN10:

    0125870736

  • Edition: 3rd
  • Format: Paperback
  • Copyright: 2006-02-16
  • Publisher: Elsevier Science

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Summary

This much admired book has been carefully revised to make crystallography even more accessible to readers who have no prior experience with crystallography and macromolecular models, or their mathematical foundations. It continues to provide clear, understandable descriptions of the principles of protein crystallography with abundant illustrations and stereo images (in full color). Coverage extends to X-ray, neutron, electron, and Laue diffraction methods, as well as NMR spectroscopy and homology modeling. Book jacket.

Table of Contents

Preface to the Third Edition xv
Preface to the Second Edition xix
Preface to the First Edition xxiii
Model and Molecule
1(6)
An Overview of Protein Crystallography
7(24)
Introduction
7(3)
Obtaining an image of a microscopic object
8(1)
Obtaining images of molecules
9(1)
A thumbnail sketch of protein crystallography
9(1)
Crystals
10(3)
The nature of crystals
10(1)
Growing crystals
11(2)
Collecting X-ray data
13(2)
Diffraction
15(4)
Simple objects
15(1)
Arrays of simple objects: Real and reciprocal lattices
16(1)
Intensities of reflections
16(1)
Arrays of complex objects
17(1)
Three-dimensional arrays
18(1)
Coordinate systems in crystallography
19(1)
The mathematics of crystallography: A brief description
20(11)
Wave equations: Periodic functions
21(2)
Complicated periodic functions: Fourier series and sums
23(1)
Structure factors: Wave descriptions of X-ray reflections
24(2)
Electron-density maps
26(1)
Electron density from structure factors
27(1)
Electron density from measured reflections
28(2)
Obtaining a model
30(1)
Protein Crystals
31(18)
Properties of protein crystals
31(4)
Introduction
31(1)
Size, structural integrity, and mosaicity
31(2)
Multiple crystalline forms
33(1)
Water content
34(1)
Evidence that solution and crystal structures are similar
35(2)
Proteins retain their function in the crystal
35(1)
X-ray structures are compatible with other structural evidence
36(1)
Other evidence
37(1)
Growing protein crystals
37(9)
Introduction
37(1)
Growing crystals: Basic procedure
38(2)
Growing derivative crystals
40(1)
Finding optimal conditions for crystal growth
41(5)
Judging crystal quality
46(1)
Mounting crystals for data collection
46(3)
Collecting Diffraction Data
49(42)
Introduction
49(1)
Geometric principles of diffraction
49(24)
The generalized unit cell
49(1)
Indices of the atomic planes in a crystal
50(5)
Conditions that produce diffraction: Bragg's law
55(2)
The reciprocal lattice
57(3)
Bragg's law in reciprocal space
60(4)
Number of measurable reflections
64(1)
Unit-cell dimensions
65(1)
Unit-cell symmetry
65(8)
Collecting X-ray diffraction data
73(16)
Introduction
73(1)
X-ray sources
73(4)
Detectors
77(3)
Cameras
80(5)
Scaling and postrefinement of intensity data
85(1)
Determining unit-cell dimensions
86(2)
Symmetry and the strategy of collecting data
88(1)
Summary
89(2)
From Diffraction Data to Electron Density
91(18)
Introduction
91(1)
Fourier sums and the Fourier transform
92(6)
One-dimensional waves
92(2)
Three-dimensional waves
94(2)
The Fourier transform: General features
96(1)
Fourier this and Fourier that: Review
97(1)
Fourier mathematics and diffraction
98(3)
Structure factor as a Fourier sum
98(1)
Electron density as a Fourier sum
99(1)
Computing electron density from data
100(1)
The phase problem
101(1)
Meaning of the Fourier equations
101(6)
Reflections as terms in a Fourier sum: Eq. (5.18)
101(3)
Computing structure factors from a model: Eq. (5.15) and Eq. (5.16)
104(1)
Systematic absences in the diffraction pattern: Eq. (5.15)
105(2)
Summary: From data to density
107(2)
Obtaining Phases
109(36)
Introduction
109(3)
Two-dimensional representation of structure factors
112(5)
Complex numbers in two dimensions
112(1)
Structure factors as complex vectors
112(3)
Electron density as a function of intensities and phases
115(2)
Isomorphous replacement
117(11)
Preparing heavy-atom derivatives
117(2)
Obtaining phases from heavy-atom data
119(5)
Locating heavy atoms in the unit cell
124(4)
Anomalous scattering
128(8)
Introduction
128(1)
Measurable effects of anomalous scattering
128(2)
Extracting phases from anomalous scattering data
130(2)
Summary
132(1)
Multiwavelength anomalous diffraction phasing
133(2)
Anomalous scattering and the hand problem
135(1)
Direct phasing: Application of methods from small-molecule crystallography
135(1)
Molecular replacement: Related proteins as phasing models
136(7)
Introduction
136(1)
Isomorphous phasing models
137(2)
Nonisomorphous phasing models
139(1)
Separate searches for orientation and location
139(2)
Monitoring the search
141(2)
Summary of molecular replacement
143(1)
Iterative improvement of phases (preview of Chapter 7)
143(2)
Obtaining and Judging the Molecular Model
145(34)
Introduction
145(1)
Iterative improvement of maps and models---overview
146(3)
First maps
149(4)
Resources for the first map
149(1)
Displaying and examining the map
150(1)
Improving the map
151(2)
The Model becomes molecular
153(6)
New phases from the molecular model
153(1)
Minimizing bias from the model
154(2)
Map fitting
156(3)
Structure refinement
159(9)
Least-squares methods
159(1)
Crystallographic refinement by least squares
160(1)
Additional refinement parameters
161(1)
Local minima and radius of convergence
162(1)
Molecular energy and motion in refinement
163(1)
Bayesian methods: Ensembles of models
164(4)
Convergence to a final model
168(5)
Producing the final map and model
168(3)
Guides to convergence
171(2)
Sharing the model
173(6)
A User's Guide to Crystallographic Models
179(32)
Introduction
179(2)
Judging the quality and usefulness of the refined model
181(11)
Structural parameters
181(2)
Resolution and precision of atomic positions
183(2)
Vibration and disorder
185(2)
Other limitations of crystallographic models
187(2)
Online validation tools: Do it yourself!
189(3)
Summary
192(1)
Reading a crystallography paper
192(17)
Introduction
192(1)
Annotated excerpts of the preliminary (8/91) paper
193(5)
Annotated excerpts from the full structure-determination (4/92) paper
198(11)
Summary
209(2)
Other Diffraction Methods
211(26)
Introduction
211(1)
Fiber diffraction
211(8)
Diffraction by amorphous materials (scattering)
219(3)
Neutron diffraction
222(5)
Electron diffraction and cryo-electron microscopy
227(4)
Laue diffraction and time-resolved crystallography
231(4)
Summary
235(2)
Other Kinds of Macromolecular Models
237(32)
Introduction
237(1)
NMR models
238(21)
Introduction
238(1)
Principles
239(12)
Assigning resonances
251(1)
Determining conformation
252(5)
PDB files for NMR models
257(1)
Judging model quality
257(2)
Homology models
259(8)
Introduction
259(1)
Principles
260(3)
Databases of homology models
263(2)
Judging model quality
265(2)
Other theoretical models
267(2)
Tools for Studying Macromolecules
269(24)
Introduction
269(1)
Computer models of molecules
269(6)
Two-dimensional images from coordinates
269(1)
Into three dimensions: Basic modeling operations
270(2)
Three-dimensional display and perception
272(1)
Types of graphical models
273(2)
Touring a molecular modeling program
275(13)
Importing and exporting coordinate files
276(2)
Loading and saving models
278(1)
Viewing models
278(2)
Editing and labeling the display
280(1)
Coloring
281(1)
Measuring
281(1)
Exploring structural change
282(1)
Exploring the molecular surface
282(4)
Exploring intermolecular interactions: Multiple models
286(1)
Displaying crystal packing
287(1)
Building models from scratch
287(1)
Scripts and macros: Automating routine structure analysis
287(1)
Other tools for studying structure
288(3)
Tools for structure analysis and validation
288(2)
Tools for modeling protein action
290(1)
Final note
291(2)
Appendix Viewing Stereo Images 293(2)
Index 295

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