Item Details

Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models

Gale Rhodes
Format
Book
Published
San Diego : Academic Press, c2000.
Edition
2nd. ed
Language
English
ISBN
0125870728
Contents
  • 1. Model and Molecule 1
  • 2. An Overview of Protein Crystallography 5
  • A. Obtaining an image of a microscopic object 6
  • B. Obtaining images of molecules 7
  • C. A thumbnail sketch of protein crystallography 7
  • II. Crystals 8
  • A. 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. Three-dimensional arrays 16
  • V. Coordinate systems in crystallography 17
  • VI. Mathematics of crystallography: A brief description 19
  • A. Wave equations: Periodic functions 19
  • B. Complicated periodic functions: Fourier series 20
  • C. Structure factors: Wave descriptions of X-ray reflections 24
  • D. 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
  • B. Size, structural integrity, and mosaicity 29
  • C. Multiple crystalline forms 31
  • D. Water content 32
  • II. 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
  • 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
  • II. Geometric principles of diffraction 45
  • A. Generalized unit cell 46
  • B. Indices of the atomic planes in a crystal 47
  • C. Conditions that produce diffraction: Bragg's law 50
  • D. Reciprocal lattice 52
  • E. Bragg's law in reciprocal space 55
  • F. Number of measurable reflections 58
  • G. Unit-cell dimensions 60
  • H. Unit-cell symmetry 60
  • III. Collecting X-ray diffraction data 64
  • B. X-ray sources 65
  • C. Detectors 69
  • D. Diffractometers and cameras 72
  • E. Scaling and postrefinement of intensity data 79
  • F. Determining unit-cell dimensions 80
  • G. Symmetry and the strategy of collecting data 82
  • 5. From Diffraction Data to Electron Density 85
  • II. Fourier series and the Fourier transform 86
  • A. One-dimensional waves 86
  • B. Three-dimensional waves 88
  • C. Fourier transform: General features 90
  • D. Fourier this and Fourier that: Review 92
  • III. Fourier mathematics and diffraction 92
  • A. Stucture factor as a Fourier series 92
  • B. Electron density as a Fourier series 94
  • C. Computing electron density from data 95
  • D. Phase problem 95
  • IV. Meaning of the Fourier equations 95
  • A. Reflections as Fourier terms: Equation (5.18) 95
  • B. Computing structure factors from a model: Equations (5.15) and (5.16) 96
  • C. Systematic absences in the diffraction pattern: Equation (5.15) 98
  • V. Summary: From data to density 100
  • 6. Obtaining Phases 101
  • II. Two-dimensional representation of structure factors 102
  • A. Complex numbers in two dimensions 102
  • B. Structure factors as complex vectors 103
  • C. Electron density as a function of intensities and phases 106
  • III. Heavy-atom method (isomorphous replacement) 107
  • A. Preparing heavy-atom derivatives 108
  • B. Obtaining phases from heavy-atom data 109
  • C. Locating heavy atoms in the unit cell 114
  • IV. Anomalous scattering 118
  • B. Measurable effects of anomalous scattering 119
  • C. Extracting phases from anomalous scattering data 120
  • E. Multiwavelength anomalous diffraction phasing 124
  • F. Anomalous scattering and the hand problem 125
  • G.g Direct phasing: Application of methods from small-molecule crystallography 126
  • V. Molecular replacement: Related proteins as phasing models 127
  • B. Isomorphous phasing models 128
  • C. Nonisomorphous phasing models 129
  • D. Separate searches for orientation and location 129
  • E. Monitoring the search 130
  • VI. Iterative improvement of phases (preview of Chapter 7) 132
  • 7. Obtaining and Judging the Molecular Model 133
  • II. Iterative improvement of maps and models: Overview 133
  • III. First maps 137
  • A. Resources for the first map 137
  • B. Displaying and examining the map 138
  • C. Improving the map 139
  • IV. Model becomes molecular 141
  • A. New phases from the molecular model 141
  • B. Minimizing bias from the model 142
  • C. Map fitting 144
  • V. Structure refinement 146
  • A. Least-squares methods 146
  • B. Crystallographic refinement 147
  • C. Additional refinement parameters 147
  • D. Local minima and radius of convergence 149
  • E. Molecular energy and motion in refinement 150
  • VI. Convergence to a final structure 151
  • A. Producing the final map and model 151
  • B. Guides to convergence 153
  • VII. Sharing the model 154
  • 8. A User's Guide to Crystallographic Models 159
  • II. Judging the quality and usefulness of the refined model 160
  • A. Structural parameters 160
  • B. Resolution and precision of atomic positions 162
  • C. Vibration and disorder 164
  • D. Other limitations of crystallographic models 166
  • III. Reading a crystallography paper 170
  • B. Annotated excerpts of the preliminary (8/91) paper 170
  • C. Annotated excerpts from the full structure determination (4/92) paper 175
  • 9. Other Diffraction Methods 187
  • II. Fiber diffraction 188
  • III. Diffraction by amorphous materials (scattering) 196
  • IV. Neutron diffraction 200
  • V. Electron diffraction 205
  • VI. Lane diffraction and time-resolved crystallography 209
  • 10. Other Kinds of Macromolecular Models 215
  • II. NMR models 216
  • C. Assigning resonances 230
  • D. Determining conformation 232
  • E. PDB files for NMR models 235
  • F. Judging model quality 235
  • III. Homology models 237
  • C. Databases of homology models 242
  • D. Judging model quality 243
  • IV. Other theoretical models 246
  • 11. Tools for Studying Macromolecules 247
  • II. Computer models of molecules 248
  • A. Two-dimensional images from coordinates 248
  • B. Into three dimensions: Basic modeling operations 249
  • C. Three-dimensional display and perception 250
  • D. Types of graphical models 251
  • III. Touring a typical molecular modeling program 252
  • A. Importing and exporting coordinates files 253
  • B. Loading and saving models 253
  • C. Viewing models 254
  • D. Editing and labeling the display 255
  • E. Coloring 256
  • F. Measuring 257
  • G. Exploring structural change 257
  • H. Exploring the molecular surface 258
  • I. Exploring intermolecular interactions: Multiple models 259
  • J. Displaying crystal packing 260
  • K. Building models from scratch 260
  • IV. Other tools for studying structure 261
  • A. Tools for structure analysis 261
  • B. Tools for modeling protein action 263.
Description
xix, 269 p., [16] p. of col. plates : ill. ; 23 cm.
Notes
Includes bibliographical references and index.
Technical Details
  • Access in Virgo Classic

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    a| Crystallography made crystal clear : b| a guide for users of macromolecular models / c| Gale Rhodes.
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    a| 2nd. ed.
    260
      
      
    a| San Diego : b| Academic Press, c| c2000.
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    a| xix, 269 p., [16] p. of col. plates : b| ill. ; c| 23 cm.
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    g| 1. t| Model and Molecule g| 1 -- g| 2. t| An Overview of Protein Crystallography g| 5 -- g| A. t| Obtaining an image of a microscopic object g| 6 -- g| B. t| Obtaining images of molecules g| 7 -- g| C. t| A thumbnail sketch of protein crystallography g| 7 -- g| II. t| Crystals g| 8 -- g| A. t| Nature of crystals g| 8 -- g| B. t| Growing crystals g| 9 -- g| III. t| Collecting X-ray data g| 10 -- g| IV. t| Diffraction g| 12 -- g| A. t| Simple objects g| 12 -- g| B. t| Arrays of simple objects: Real and reciprocal lattices g| 13 -- g| C. t| Intensities of reflections g| 14 -- g| D. t| Arrays of complex objects g| 15 -- g| E. t| Three-dimensional arrays g| 16 -- g| V. t| Coordinate systems in crystallography g| 17 -- g| VI. t| Mathematics of crystallography: A brief description g| 19 -- g| A. t| Wave equations: Periodic functions g| 19 -- g| B. t| Complicated periodic functions: Fourier series g| 20 -- g| C. t| Structure factors: Wave descriptions of X-ray reflections g| 24 -- g| D. t| Electron-density maps g| 24 -- g| E. t| Electron density from structure factors g| 25 -- g| F. t| Electron density from measured reflections g| 27 -- g| G. t| Obtaining a model g| 28 -- g| 3. t| Protein Crystals g| 29 -- g| I. t| Properties of protein crystals g| 29 -- g| B. t| Size, structural integrity, and mosaicity g| 29 -- g| C. t| Multiple crystalline forms g| 31 -- g| D. t| Water content g| 32 -- g| II. t| Evidence that solution and crystal structures are similar g| 33 -- g| A. t| Proteins retain their function in the crystal g| 33 -- g| B. t| X-ray structures are compatible with other structural evidence g| 34 -- g| C. t| Other evidence g| 34 -- g| III. t| Growing protein crystals g| 35 -- g| B. t| Growing crystals: Basic procedure g| 35 -- g| C. t| Growing derivative crystals g| 37 -- g| D. t| Finding optimal conditions for crystal growth g| 37 -- g| IV. t| Judging crystal quality g| 41 -- g| V. t| Mounting crystals for data collection g| 43 -- g| 4. t| Collecting Diffraction Data g| 45 -- g| II. t| Geometric principles of diffraction g| 45 -- g| A. t| Generalized unit cell g| 46 -- g| B. t| Indices of the atomic planes in a crystal g| 47 -- g| C. t| Conditions that produce diffraction: Bragg's law g| 50 -- g| D. t| Reciprocal lattice g| 52 -- g| E. t| Bragg's law in reciprocal space g| 55 -- g| F. t| Number of measurable reflections g| 58 -- g| G. t| Unit-cell dimensions g| 60 -- g| H. t| Unit-cell symmetry g| 60 -- g| III. t| Collecting X-ray diffraction data g| 64 -- g| B. t| X-ray sources g| 65 -- g| C. t| Detectors g| 69 -- g| D. t| Diffractometers and cameras g| 72 -- g| E. t| Scaling and postrefinement of intensity data g| 79 -- g| F. t| Determining unit-cell dimensions g| 80 -- g| G. t| Symmetry and the strategy of collecting data g| 82 -- g| 5. t| From Diffraction Data to Electron Density g| 85 -- g| II. t| Fourier series and the Fourier transform g| 86 -- g| A. t| One-dimensional waves g| 86 -- g| B. t| Three-dimensional waves g| 88 -- g| C. t| Fourier transform: General features g| 90 -- g| D. t| Fourier this and Fourier that: Review g| 92 -- g| III. t| Fourier mathematics and diffraction g| 92 -- g| A. t| Stucture factor as a Fourier series g| 92 -- g| B. t| Electron density as a Fourier series g| 94 -- g| C. t| Computing electron density from data g| 95 -- g| D. t| Phase problem g| 95 -- g| IV. t| Meaning of the Fourier equations g| 95 -- g| A. t| Reflections as Fourier terms: Equation (5.18) g| 95 -- g| B. t| Computing structure factors from a model: Equations (5.15) and (5.16) g| 96 -- g| C. t| Systematic absences in the diffraction pattern: Equation (5.15) g| 98 -- g| V. t| Summary: From data to density g| 100 -- g| 6. t| Obtaining Phases g| 101 -- g| II. t| Two-dimensional representation of structure factors g| 102 -- g| A. t| Complex numbers in two dimensions g| 102 -- g| B. t| Structure factors as complex vectors g| 103 -- g| C. t| Electron density as a function of intensities and phases g| 106 -- g| III. t| Heavy-atom method (isomorphous replacement) g| 107 -- g| A. t| Preparing heavy-atom derivatives g| 108 -- g| B. t| Obtaining phases from heavy-atom data g| 109 -- g| C. t| Locating heavy atoms in the unit cell g| 114 -- g| IV. t| Anomalous scattering g| 118 -- g| B. t| Measurable effects of anomalous scattering g| 119 -- g| C. t| Extracting phases from anomalous scattering data g| 120 -- g| E. t| Multiwavelength anomalous diffraction phasing g| 124 -- g| F. t| Anomalous scattering and the hand problem g| 125 -- g| G.g t| Direct phasing: Application of methods from small-molecule crystallography g| 126 -- g| V. t| Molecular replacement: Related proteins as phasing models g| 127 -- g| B. t| Isomorphous phasing models g| 128 -- g| C. t| Nonisomorphous phasing models g| 129 -- g| D. t| Separate searches for orientation and location g| 129 -- g| E. t| Monitoring the search g| 130 -- g| VI. t| Iterative improvement of phases (preview of Chapter 7) g| 132 -- g| 7. t| Obtaining and Judging the Molecular Model g| 133 -- g| II. t| Iterative improvement of maps and models: Overview g| 133 -- g| III. t| First maps g| 137 -- g| A. t| Resources for the first map g| 137 -- g| B. t| Displaying and examining the map g| 138 -- g| C. t| Improving the map g| 139 -- g| IV. t| Model becomes molecular g| 141 -- g| A. t| New phases from the molecular model g| 141 -- g| B. t| Minimizing bias from the model g| 142 -- g| C. t| Map fitting g| 144 -- g| V. t| Structure refinement g| 146 -- g| A. t| Least-squares methods g| 146 -- g| B. t| Crystallographic refinement g| 147 -- g| C. t| Additional refinement parameters g| 147 -- g| D. t| Local minima and radius of convergence g| 149 -- g| E. t| Molecular energy and motion in refinement g| 150 -- g| VI. t| Convergence to a final structure g| 151 -- g| A. t| Producing the final map and model g| 151 -- g| B. t| Guides to convergence g| 153 -- g| VII. t| Sharing the model g| 154 -- g| 8. t| A User's Guide to Crystallographic Models g| 159 -- g| II. t| Judging the quality and usefulness of the refined model g| 160 -- g| A. t| Structural parameters g| 160 -- g| B. t| Resolution and precision of atomic positions g| 162 -- g| C. t| Vibration and disorder g| 164 -- g| D. t| Other limitations of crystallographic models g| 166 -- g| III. t| Reading a crystallography paper g| 170 -- g| B. t| Annotated excerpts of the preliminary (8/91) paper g| 170 -- g| C. t| Annotated excerpts from the full structure determination (4/92) paper g| 175 -- g| 9. t| Other Diffraction Methods g| 187 -- g| II. t| Fiber diffraction g| 188 -- g| III. t| Diffraction by amorphous materials (scattering) g| 196 -- g| IV. t| Neutron diffraction g| 200 -- g| V. t| Electron diffraction g| 205 -- g| VI. t| Lane diffraction and time-resolved crystallography g| 209 -- g| 10. t| Other Kinds of Macromolecular Models g| 215 -- g| II. t| NMR models g| 216 -- g| C. t| Assigning resonances g| 230 -- g| D. t| Determining conformation g| 232 -- g| E. t| PDB files for NMR models g| 235 -- g| F. t| Judging model quality g| 235 -- g| III. t| Homology models g| 237 -- g| C. t| Databases of homology models g| 242 -- g| D. t| Judging model quality g| 243 -- g| IV. t| Other theoretical models g| 246 -- g| 11. t| Tools for Studying Macromolecules g| 247 -- g| II. t| Computer models of molecules g| 248 -- g| A. t| Two-dimensional images from coordinates g| 248 -- g| B. t| Into three dimensions: Basic modeling operations g| 249 -- g| C. t| Three-dimensional display and perception g| 250 -- g| D. t| Types of graphical models g| 251 -- g| III. t| Touring a typical molecular modeling program g| 252 -- g| A. t| Importing and exporting coordinates files g| 253 -- g| B. t| Loading and saving models g| 253 -- g| C. t| Viewing models g| 254 -- g| D. t| Editing and labeling the display g| 255 -- g| E. t| Coloring g| 256 -- g| F. t| Measuring g| 257 -- g| G. t| Exploring structural change g| 257 -- g| H. t| Exploring the molecular surface g| 258 -- g| I. t| Exploring intermolecular interactions: Multiple models g| 259 -- g| J. t| Displaying crystal packing g| 260 -- g| K. t| Building models from scratch g| 260 -- g| IV. t| Other tools for studying structure g| 261 -- g| A. t| Tools for structure analysis g| 261 -- g| B. t| Tools for modeling protein action g| 263.
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    a| X-ray crystallography.
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    a| Macromolecules x| Structure.
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    a| Proteins x| Structure.
    999
      
      
    a| QP519.9 .X72 R48 2000 w| LC i| X004527138 l| BY-REQUEST m| IVY t| BOOK

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