+612 9045 4394
 
CHECKOUT
Crystallography Made Crystal Clear, third edition : A Guide for Users of Macromolecular Models - Gale Rhodes

Crystallography Made Crystal Clear, third edition

A Guide for Users of Macromolecular Models

Paperback

Published: 13th March 2006
Ships: 15 business days
15 business days
$94.90
or 4 easy payments of $23.73 with Learn more

Crystallography Made Crystal Clear makes crystallography accessible to readers who have no prior knowledge of the field or its mathematical basis. This is the most comprehensive and concise reference for beginning Macromolecular crystallographers, written by a leading expert in the field. Rhodes' uses visual and geometric models to help readers understand the mathematics that form the basis of x-ray crystallography. He has invested a great deal of time and effort on World Wide Web tools for users of models, including beginning-level tutorials in molecular modeling on personal computers. Rhodes' personal CMCC Home Page also provides access to tools and links to resources discussed in the text. Most significantly, the final chapter introduces the reader to macromolecular modeling on personal computers-featuring SwissPdbViewer, a free, powerful modeling program now available for PC, Power Macintosh, and Unix computers. This updated and expanded new edition uses attractive four-color art, web tool access for further study, and concise language to explain the basis of X-ray crystallography, increasingly vital in today's research labs.
* Helps readers to understand where models come from, so they don't use them blindly and
inappropriately
* Provides many visual and geometric models for understanding a largely mathematical method
* Allows readers to judge whether recently published models are of sufficiently high quality and detail to be useful in their own work
* Allows readers to study macromolecular structure independently and in an open-ended fashion on their own computers, without being limited to textbook or journals illustrations
* Provides access to web tools in a format that will not go out of date. Links will be updated and added as existing resources change location or are added

Praise for the first edition "Well-written...in my opinion is now the best reference for noncrystallographers who want to know more about X-ray diffraction and the data that result from it." -AMERICAN JOURNAL OF PHYSIOLOGY

Preface to the Third Editionp. xv
Preface to the Second Editionp. xix
Preface to the First Editionp. xxiii
Model and Moleculep. 1
An Overview of Protein Crystallographyp. 7
Introductionp. 7
Obtaining an image of a microscopic objectp. 8
Obtaining images of moleculesp. 9
A thumbnail sketch of protein crystallographyp. 9
Crystalsp. 10
The nature of crystalsp. 10
Growing crystalsp. 11
Collecting X-ray datap. 13
Diffractionp. 15
Simple objectsp. 15
Arrays of simple objects: Real and reciprocal latticesp. 16
Intensities of reflectionsp. 16
Arrays of complex objectsp. 17
Three-dimensional arraysp. 18
Coordinate systems in crystallographyp. 19
The mathematics of crystallography: A brief descriptionp. 20
Wave equations: Periodic functionsp. 21
Complicated periodic functions: Fourier series and sumsp. 23
Structure factors: Wave descriptions of X-ray reflectionsp. 24
Electron-density mapsp. 26
Electron density from structure factorsp. 27
Electron density from measured reflectionsp. 28
Obtaining a modelp. 30
Protein Crystalsp. 31
Properties of protein crystalsp. 31
Introductionp. 31
Size, structural integrity, and mosaicityp. 31
Multiple crystalline formsp. 33
Water contentp. 34
Evidence that solution and crystal structures are similarp. 35
Proteins retain their function in the crystalp. 35
X-ray structures are compatible with other structural evidencep. 36
Other evidencep. 37
Growing protein crystalsp. 37
Introductionp. 37
Growing crystals: Basic procedurep. 38
Growing derivative crystalsp. 40
Finding optimal conditions for crystal growthp. 41
Judging crystal qualityp. 46
Mounting crystals for data collectionp. 46
Collecting Diffraction Datap. 49
Introductionp. 49
Geometric principles of diffractionp. 49
The generalized unit cellp. 49
Indices of the atomic planes in a crystalp. 50
Conditions that produce diffraction: Bragg's lawp. 55
The reciprocal latticep. 57
Bragg's law in reciprocal spacep. 60
Number of measurable reflectionsp. 64
Unit-cell dimensionsp. 65
Unit-cell symmetryp. 65
Collecting X-ray diffraction datap. 73
Introductionp. 73
X-ray sourcesp. 73
Detectorsp. 77
Camerasp. 80
Scaling and postrefinement of intensity datap. 85
Determining unit-cell dimensionsp. 86
Symmetry and the strategy of collecting datap. 88
Summaryp. 89
From Diffraction Data to Electron Densityp. 91
Introductionp. 91
Fourier sums and the Fourier transformp. 92
One-dimensional wavesp. 92
Three-dimensional wavesp. 94
The Fourier transform: General featuresp. 96
Fourier this and Fourier that: Reviewp. 97
Fourier mathematics and diffractionp. 98
Structure factor as a Fourier sump. 98
Electron density as a Fourier sump. 99
Computing electron density from datap. 100
The phase problemp. 101
Meaning of the Fourier equationsp. 101
Reflections as terms in a Fourier sum: Eq. (5.18)p. 101
Computing structure factors from a model: Eq. (5.15) and Eq. (5.16)p. 104
Systematic absences in the diffraction pattern: Eq. (5.15)p. 105
Summary: From data to densityp. 107
Obtaining Phasesp. 109
Introductionp. 109
Two-dimensional representation of structure factorsp. 112
Complex numbers in two dimensionsp. 112
Structure factors as complex vectorsp. 112
Electron density as a function of intensities and phasesp. 115
Isomorphous replacementp. 117
Preparing heavy-atom derivativesp. 117
Obtaining phases from heavy-atom datap. 119
Locating heavy atoms in the unit cellp. 124
Anomalous scatteringp. 128
Introductionp. 128
Measurable effects of anomalous scatteringp. 128
Extracting phases from anomalous scattering datap. 130
Summaryp. 132
Multiwavelength anomalous diffraction phasingp. 133
Anomalous scattering and the hand problemp. 135
Direct phasing: Application of methods from small-molecule crystallographyp. 135
Molecular replacement: Related proteins as phasing modelsp. 136
Introductionp. 136
Isomorphous phasing modelsp. 137
Nonisomorphous phasing modelsp. 139
Separate searches for orientation and locationp. 139
Monitoring the searchp. 141
Summary of molecular replacementp. 143
Iterative improvement of phases (preview of Chapter 7)p. 143
Obtaining and Judging the Molecular Modelp. 145
Introductionp. 145
Iterative improvement of maps and models-overviewp. 146
First mapsp. 149
Resources for the first mapp. 149
Displaying and examining the mapp. 150
Improving the mapp. 151
The Model becomes molecularp. 153
New phases from the molecular modelp. 153
Minimizing bias from the modelp. 154
Map fittingp. 156
Structure refinementp. 159
Least-squares methodsp. 159
Crystallographic refinement by least squaresp. 160
Additional refinement parametersp. 161
Local minima and radius of convergencep. 162
Molecular energy and motion in refinementp. 163
Bayesian methods: Ensembles of modelsp. 164
Convergence to a final modelp. 168
Producing the final map and modelp. 168
Guides to convergencep. 171
Sharing the modelp. 173
A User's Guide to Crystallographic Modelsp. 179
Introductionp. 179
Judging the quality and usefulness of the refined modelp. 181
Structural parametersp. 181
Resolution and precision of atomic positionsp. 183
Vibration and disorderp. 185
Other limitations of crystallographic modelsp. 187
Online validation tools: Do it yourself!p. 189
Summaryp. 192
Reading a crystallography paperp. 192
Introductionp. 192
Annotated excerpts of the preliminary (8/91) paperp. 193
Annotated excerpts from the full structure-determination (4/92) paperp. 198
Summaryp. 209
Other Diffraction Methodsp. 211
Introductionp. 211
Fiber diffractionp. 211
Diffraction by amorphous materials (scattering)p. 219
Neutron diffractionp. 222
Electron diffraction and cryo-electron microscopyp. 227
Laue diffraction and time-resolved crystallographyp. 231
Summaryp. 235
Other Kinds of Macromolecular Modelsp. 237
Introductionp. 237
NMR modelsp. 238
Introductionp. 238
Principlesp. 239
Assigning resonancesp. 251
Determining conformationp. 252
PDB files for NMR modelsp. 257
Judging model qualityp. 257
Homology modelsp. 259
Introductionp. 259
Principlesp. 260
Databases of homology modelsp. 263
Judging model qualityp. 265
Other theoretical modelsp. 267
Tools for Studying Macromoleculesp. 269
Introductionp. 269
Computer models of moleculesp. 269
Two-dimensional images from coordinatesp. 269
Into three dimensions: Basic modeling operationsp. 270
Three-dimensional display and perceptionp. 272
Types of graphical modelsp. 273
Touring a molecular modeling programp. 275
Importing and exporting coordinate filesp. 276
Loading and saving modelsp. 278
Viewing modelsp. 278
Editing and labeling the displayp. 280
Coloringp. 281
Measuringp. 281
Exploring structural changep. 282
Exploring the molecular surfacep. 282
Exploring intermolecular interactions: Multiple modelsp. 286
Displaying crystal packingp. 287
Building models from scratchp. 287
Scripts and macros: Automating routine structure analysisp. 287
Other tools for studying structurep. 288
Tools for structure analysis and validationp. 288
Tools for modeling protein actionp. 290
Final notep. 291
Viewing Stereo Imagesp. 293
Indexp. 295
Table of Contents provided by Ingram. All Rights Reserved.

ISBN: 9780125870733
ISBN-10: 0125870736
Series: Complementary Science
Audience: Tertiary; University or College
Format: Paperback
Language: English
Number Of Pages: 352
Published: 13th March 2006
Publisher: Elsevier Science Publishing Co Inc
Country of Publication: US
Dimensions (cm): 22.9 x 15.7  x 1.8
Weight (kg): 0.58
Edition Number: 3
Edition Type: Revised