Crystallography made crystal clear: a guide for users of macromolecular models
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier / Academic Press
2009
|
| Edition: | 3. ed., [Nachdr.] |
| Series: | Complementary science series
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXV, 306 S. Ill., graph. Darst. |
| ISBN: | 0125870736 9780125870733 |
Staff View
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| 245 | 1 | 0 | |a Crystallography made crystal clear |b a guide for users of macromolecular models |c Gale Rhodes |
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| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier / Academic Press |c 2009 | |
| 300 | |a XXV, 306 S. |b Ill., graph. Darst. | ||
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Record in the Search Index
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|---|---|
| adam_text | Contents
Preface
to the Third Edition
.............................................. xv
Preface to the Second Edition
............................................ xix
Preface to the First Edition
............................................... xxiii
1
Model and Molecule
1
2
An Overview of Protein Crystallography
7
2.1
Introduction
................................................... 7
2.1.1
Obtaining an image of a microscopic object
.................. 8
2.1.2
Obtaining images of molecules
............................ 9
2.1.3
A thumbnail sketch of protein crystallography
................ 9
2.2
Crystals
...................................................... 10
2.2.1
The nature of crystals
.................................... 10
2.2.2
Growing crystals
........................................ 11
2.3
Collecting X-ray data
........................................... 13
2.4
Diffraction
.................................................... 15
2.4.1
Simple objects
.......................................... 15
2.4.2
Arrays of simple objects: Real and reciprocal lattices
........... 16
2.4.3
Intensities of reflections
.................................. 16
2.4.4
Arrays of complex objects
................................ 17
2.4.5
Three-dimensional arrays
................................. 18
2.5
Coordinate systems in crystallography
.............................. 19
2.6
The mathematics of crystallography: A brief description
............... 20
2.6.1
Wave equations: Periodic functions
......................... 21
2.6.2
Complicated periodic functions: Fourier series and sums
........ 23
2.6.3
Structure factors: Wave descriptions of X-ray reflections
........ 24
2.6.4
Electron-density maps
.................................... 26
2.6.5
Electron density from structure factors
...................... 27
2.6.6
Electron density from measured reflections
................... 28
2.6.7
Obtaining a model
....................................... 30
ІХ
Contents
Protein
Crystals
31
3.1
Properties of protein crystals
...................................... 31
3.1.1
Introduction
............................................ 31
3.1.2
Size, structural integrity, and mosaicity
...................... 31
3.1.3
Multiple crystalline forms
................................. 33
3.1.4
Water content
.......................................... 34
3.2
Evidence that solution and crystal structures are similar
................ 35
3.2.1
Proteins retain their function in the crystal
................... 35
3.2.2
X-ray structures are compatible with other structural evidence
... 36
3.2.3
Other evidence
......................................... 37
3.3
Growing protein crystals
......................................... 37
3.3.1
Introduction
............................................ 37
3.3.2
Growing crystals: Basic procedure
.......................... 38
3.3.3
Growing derivative crystals
............................... 40
3.3.4
Finding optimal conditions for crystal growth
................. 41
3.4
Judging crystal quality
.......................................... 46
3.5
Mounting crystals for data collection
............................... 46
Collecting Diffraction Data
49
4.1
Introduction
................................................... 49
4.2
Geometric principles of diffraction
................................. 49
4.2.1
The generalized unit cell
.................................. 49
4.2.2
Indices of the atomic planes in a crystal
..................... 50
4.2.3
Conditions that produce diffraction: Bragg s law
.............. 55
4.2.4
The reciprocal lattice
..................................... 57
4.2.5
Bragg s law in reciprocal space
............................ 60
4.2.6
Number of measurable reflections
.......................... 64
4.2.7
Unit-cell dimensions
..................................... 65
4.2.8
Unit-cell symmetry
...................................... 65
4.3
Collecting X-ray diffraction data
.................................. 73
4.3.1
Introduction
............................................ 73
4.3.2
X-ray sources
.......................................... 73
4.3.3
Detectors
.............................................. 77
4.3.4
Cameras
............................................... 80
4.3.5
Scaling and postrefinement of intensity data
.................. 85
4.3.6
Determining unit-cell dimensions
.......................... 86
4.3.7
Symmetry and the strategy of collecting data
................. 88
4.4
Summary
..................................................... 89
From Diffraction Data to Electron Density 91
5.1
Introduction
................................................... 91
5.2
Fourier sums and the Fourier transform
............................. 92
5.2.1
One-dimensional waves
.................................. 92
5.2.2
Three-dimensional waves
................................. 94
Contents xi
5.2.3
The Fourier transform: General features
..................... 96
5.2.4
Fourier this and Fourier that: Review
........................ 97
5.3
Fourier mathematics and diffraction
................................ 98
5.3.1
Structure factor as a Fourier sum
........................... 98
5.3.2
Electron density as a Fourier sum
.......................... 99
5.3.3
Computing electron density from data
....................... 100
5.3.4
The phase problem
...................................... 101
5.4
Meaning of the Fourier equations
.................................. 101
5.4.1
Reflections as terms in a Fourier sum: Eq.
(5.18).............. 101
5.4.2
Computing structure factors from a model: Eq.
(5.15)
and Eq.
(5.16).......................................... 104
5.4.3
Systematic absences in the diffraction pattern: Eq.
(5.15) ....... 105
5.5
Summary: From data to density
................................... 107
6
Obtaining Phases
109
6.1
Introduction
................................................... 109
6.2
Two-dimensional representation of structure factors
................... 112
6.2.1
Complex numbers in two dimensions
....................... 112
6.2.2
Structure factors as complex vectors
........................ 112
6.2.3
Electron density as a function of intensities and phases
......... 115
6.3
Isomorphous replacement
........................................ 117
6.3.1
Preparing heavy-atom derivatives
.......................... 117
6.3.2
Obtaining phases from heavy-atom data
..................... 119
6.3.3
Locating heavy atoms in the unit cell
........................ 124
6.4
Anomalous scattering
........................................... 128
6.4.1
Introduction
............................................ 128
6.4.2
Measurable effects of anomalous scattering
.................. 128
6.4.3
Extracting phases from anomalous scattering data
............. 130
6.4.4
Summary
.............................................. 132
6.4.5
Multiwavelength anomalous diffraction phasing
............... 133
6.4.6
Anomalous scattering and the hand problem
.................. 135
6.4.7
Direct phasing: Application of methods from small-molecule
crystallography
......................................... 135
6.5
Molecular replacement: Related proteins as phasing models
............ 136
6.5.1
Introduction
............................................ 136
6.5.2
Isomorphous phasing models
.............................. 137
6.5.3
Nonisomorphous phasing models
.......................... 139
6.5.4
Separate searches for orientation and location
................. 139
6.5.5
Monitoring the search
.................................... 141
6.5.6
Summary of molecular replacement
......................... 143
6.6
Iterative improvement of phases (preview of Chapter
7)................ 143
7
Obtaining and Judging the Molecular Model
145
7.1
Introduction
................................................... 145
7.2
Iterative improvement of maps and models
—
overview
................ 146
xii
Contents
7.3
First maps
.................................................... 149
7.3.1
Resources for the first map
................................
1
49
7.3.2
Displaying and examining the map
......................... 150
7.3.3
Improving the map
...................................... 151
7.4
The Model becomes molecular
.................................... 153
7.4.1
New phases from the molecular model
...................... 153
7.4.2
Minimizing bias from the model
........................... 154
7.4.3
Map fitting
............................................. 156
7.5
Structure refinement
............................................ ! 59
7.5.1
Least-squares methods
................................... 159
7.5.2
Crystallographic refinement by least squares
.................. 160
7.5.3
Additional refinement parameters
........................... 161
7.5.4
Local minima and radius of convergence
.................... 162
7.5.5
Molecular energy and motion in refinement
.................. 163
7.5.6
Bayesian methods: Ensembles of models
.................... 164
7.6
Convergence to a final model
..................................... 168
7.6.1
Producing the final map and model
......................... 168
7.6.2
Guides to convergence
................................... 171
7.7
Sharing the model
.............................................. 173
8
A User s Guide to Crystallographic Models
179
8.1
Introduction
................................................... 179
8.2
Judging the quality and usefulness of the refined model
................ 181
8.2.1
Structural parameters
.................................... 181
8.2.2
Resolution and precision of atomic positions
................. 183
8.2.3
Vibration and disorder
................................... 185
8.2.4
Other limitations of crystallographic models
.................. 187
8.2.5
Online validation tools: Do it yourself!
...................... 189
8.2.6
Summary
.............................................. 192
8.3
Reading a crystallography paper
................................... 192
8.3.1
Introduction
............................................ 192
8.3.2
Annotated excerpts of the preliminary
(8/91)
paper
............ 193
8.3.3
Annotated excerpts from the full structure-determination
(4/92)
paper
............................................ 198
8.4
Summary
..................................................... 209
9
Other Diffraction Methods
211
9.1
Introduction
................................................... 211
9.2
Fiber diffraction
................................................ 211
9.3
Diffraction by amorphous materials (scattering)
...................... 219
9.4
Neutron diffraction
............................................. 222
9.5
Electron diffraction and cryo-electron microscopy
.................... 227
9.6 Laue
diffraction and time-resolved crystallography
.................... 231
9.7
Summary
..................................................... 235
Contents xiii
10
Other
Kinds
of Macromolecular
Models 237
10.1
Introduction...................................................
237
10.2 NMR
models..................................................
238
10.2.1
Introduction
............................................ 238
10.2.2
Principles
.............................................. 239
10.2.3
Assigning resonances
.................................... 251
10.2.4
Determining conformation
................................ 252
10.2.5
PDB files for NMR models
............................... 257
10.2.6
Judging model quality
.................................... 257
10.3
Homology models
.............................................. 259
10.3.1
Introduction
............................................ 259
10.3.2
Principles
.............................................. 260
10.3.3
Databases of homology models
............................ 263
10.3.4
Judging model quality
.................................... 265
10.4
Other theoretical models
......................................... 267
11
Tools for Studying Macromolecules
269
11.1
Introduction
................................................... 269
11.2
Computer models of molecules
.................................... 269
11.2.1
Two-dimensional images from coordinates
................... 269
11.2.2
Into three dimensions: Basic modeling operations
............. 270
11.2.3
Three-dimensional display and perception
................... 272
11.2.4
Types of graphical models
................................ 273
11.3
Touring a molecular modeling program
............................. 275
11.3.1
Importing and exporting coordinate files
..................... 276
11.3.2
Loading and saving models
............................... 278
11.3.3
Viewing models
......................................... 278
11.3.4
Editing and labeling the display
............................ 280
11.3.5
Coloring
............................................... 281
11.3.6
Measuring
............................................. 281
11.3.7
Exploring structural change
............................... 282
11.3.8
Exploring the molecular surface
............................ 282
11.3.9
Exploring intermolecular interactions: Multiple models
......... 286
11.3.10
Displaying crystal packing
................................ 287
11.3.11
Building models from scratch
.............................. 287
11.3.12
Scripts and macros: Automating routine structure analysis
....... 287
11.4
Other tools for studying structure
.................................. 288
11.4.1
Tools for structure analysis and validation
.................... 288
11.4.2
Tools for modeling protein action
.......................... 290
11.5
Final note
..................................................... 291
Appendix Viewing Stereo Images
293
Index
295
|
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| classification_tum | CHE 806f |
| ctrlnum | (OCoLC)604175448 (DE-599)BVBBV036636348 |
| discipline | Biologie Chemie |
| edition | 3. ed., [Nachdr.] |
| format | Book |
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| id | DE-604.BV036636348 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:44:42Z |
| institution | BVB |
| isbn | 0125870736 9780125870733 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-020556063 |
| oclc_num | 604175448 |
| open_access_boolean | |
| owner | DE-20 DE-703 |
| owner_facet | DE-20 DE-703 |
| physical | XXV, 306 S. Ill., graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | Elsevier / Academic Press |
| record_format | marc |
| series2 | Complementary science series |
| spelling | Rhodes, Gale Verfasser aut Crystallography made crystal clear a guide for users of macromolecular models Gale Rhodes 3. ed., [Nachdr.] Amsterdam [u.a.] Elsevier / Academic Press 2009 XXV, 306 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Complementary science series X-ray crystallography Macromolecules Structure Proteins Structure Proteine (DE-588)4076388-2 gnd rswk-swf Kristallographie (DE-588)4033217-2 gnd rswk-swf Chemische Struktur (DE-588)4009857-6 gnd rswk-swf Makromolekül (DE-588)4037172-4 gnd rswk-swf Proteine (DE-588)4076388-2 s Chemische Struktur (DE-588)4009857-6 s DE-604 Kristallographie (DE-588)4033217-2 s Makromolekül (DE-588)4037172-4 s Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020556063&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Rhodes, Gale Crystallography made crystal clear a guide for users of macromolecular models X-ray crystallography Macromolecules Structure Proteins Structure Proteine (DE-588)4076388-2 gnd Kristallographie (DE-588)4033217-2 gnd Chemische Struktur (DE-588)4009857-6 gnd Makromolekül (DE-588)4037172-4 gnd |
| subject_GND | (DE-588)4076388-2 (DE-588)4033217-2 (DE-588)4009857-6 (DE-588)4037172-4 |
| title | Crystallography made crystal clear a guide for users of macromolecular models |
| title_auth | Crystallography made crystal clear a guide for users of macromolecular models |
| title_exact_search | Crystallography made crystal clear a guide for users of macromolecular models |
| title_full | Crystallography made crystal clear a guide for users of macromolecular models Gale Rhodes |
| title_fullStr | Crystallography made crystal clear a guide for users of macromolecular models Gale Rhodes |
| title_full_unstemmed | Crystallography made crystal clear a guide for users of macromolecular models Gale Rhodes |
| title_short | Crystallography made crystal clear |
| title_sort | crystallography made crystal clear a guide for users of macromolecular models |
| title_sub | a guide for users of macromolecular models |
| topic | X-ray crystallography Macromolecules Structure Proteins Structure Proteine (DE-588)4076388-2 gnd Kristallographie (DE-588)4033217-2 gnd Chemische Struktur (DE-588)4009857-6 gnd Makromolekül (DE-588)4037172-4 gnd |
| topic_facet | X-ray crystallography Macromolecules Structure Proteins Structure Proteine Kristallographie Chemische Struktur Makromolekül |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020556063&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT rhodesgale crystallographymadecrystalclearaguideforusersofmacromolecularmodels |