Crystals, X-rays and proteins: comprehensive protein crystallography
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oxford [u.a.]
Oxford Univ. Press
2011
|
| Ausgabe: | 1. publ. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XVII, 621 S. Ill., graph. Darst. |
| ISBN: | 9780199559046 |
Internformat
MARC
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| 100 | 1 | |a Sherwood, Dennis |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Crystals, X-rays and proteins |b comprehensive protein crystallography |c Dennis Sherwood ; Jon Cooper |
| 250 | |a 1. publ. | ||
| 264 | 1 | |a Oxford [u.a.] |b Oxford Univ. Press |c 2011 | |
| 300 | |a XVII, 621 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
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| 689 | 0 | 1 | |a Röntgenstrukturanalyse |0 (DE-588)4137203-7 |D s |
| 689 | 0 | |5 DE-604 | |
| 700 | 1 | |a Cooper, Jonathan M. |e Verfasser |4 aut | |
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Datensatz im Suchindex
| _version_ | 1804143168605650944 |
|---|---|
| adam_text | Contents
List of symbols
xiv
PART I FUNDAMENTALS
1
The crystalline state and its study
3
1.1
States of matter
3
1.2
Anisotropy
4
1.3
The significance of order
6
1.4
Crystals
9
1.5
Solids which are not crystals
11
1.6
Crystal defects
13
1.7
Analysing the structure of crystals and molecules
13
1.8
Why do we use X-rays?
17
1.9
Why do we use diffraction?
20
1.10
Protein crystals
20
Summary
21
Bibliography
21
2
Vector analysis and complex algebra
23
VECTORS
23
2.1
What is a vector?
23
2.2
Vector addition
25
2.3
Multiplication by a scalar
27
2.4
Unit vectors
27
2.5
Components
30
2.6
Vector subtraction
32
2.7
Multiplication by a vector to give a scalar
33
2.8
Multiplication by a vector to give a vector
36
2.9
The scalar triple product and the vector triple product
39
COMPLEX ALGEBRA
42
2.10
What is a complex number?
43
2.11
The Argand diagram
44
2.12
The addition of complex numbers
46
2.13
Multiplication of complex numbers
47
2.14
The complex conjugate
48
2.15
The complex exponential representation
49
2.16
Complex exponentials and trigonometric functions
51
Summary
52
Appendix: Determinants
55
Bibliography
57
viii Contents
3
Crystal systematics
58
3.1
What is a crystal?
58
3.2
Symmetry
61
3.3
The description of the lattice
62
3.4
Crystal directions
72
3.5
Lattice planes
72
3.6
Symmetry operations and symmetry elements
76
3.7
Point groups and
Laue
groups
84
3.8
Space groups
87
Summary
91
Bibliography
92
4
Waves and electromagnetic radiation
93
4.1
Mathematical functions
93
4.2
What is a wave?
94
4.3
The mathematical description of a wave
97
4.4
The wave equation
104
4.5
The solution of the wave equation
106
4.6
The principle of superposition 111
4.7
Phase
114
4.8
Waves and complex exponentials
118
4.9
Intensity
120
4.10
Waves which are not plane
121
4.11
Electromagnetic waves
122
4.12
The form of electromagnetic waves
124
4.13
The interaction of electromagnetic radiation with matter
126
Summary
131
Bibliography
132
5
Fourier transforms and convolutions
133
5.1
Integrals
133
5.2
Curve sketching
135
5.3
Fourier transforms
141
5.4
Mathematical conventions and physical reality
146
5.5
The inverse transform
148
5.6
Real space and Fourier space
151
5.7
Delta functions
152
5.8
Fourier transforms and delta functions
154
5.9
Symmetrical and antisymmetrical functions
164
5.10
Convolutions
166
5.11
The Fourier transform of a convolution
172
5.12
The Patterson function
173
Summary
176
Appendix I: Proof of Fourier s theorem
179
Appendix II: Proof of convolution theorem
180
Bibliography
183
Contents ix
6
Diffraction
184
6.1
The interaction of waves with obstacles
184
6.2
The diffraction of water waves
185
6.3
Diffraction and information
189
6.4
The diffraction of light
190
6.5
X-ray diffraction
192
6.6
The mathematics of diffraction
192
6.7
Diffraction and Fourier transforms
198
6.8
The significance of the Fourier transform
200
6.9
Fourier transforms and phase
203
6.10
Fourier transforms and the wave equation
205
6.11
Fourier transforms and information
206
6.12
The inverse transform
208
6.13
The significance of the inverse transform
210
6.14
Experimental limitations
213
Summary
214
Bibliography
215
Review I
216
PART II DIFFRACTION THEORY
7
Diffraction by one-dimensional obstacles
221
7.1
The geometrical arrangement
221
7.2
One narrow slit
224
7.3
One wide slit
226
7.4
Two narrow slits
227
7.5
Young s experiment
228
7.6
Two wide slits
232
7.7
Three narrow slits
235
7.8
Three wide slits
236
7.9 N
narrow slits
237
7.10 N
wide slits
238
7.11
An infinite number of narrow slits
239
7.12
An infinite number of wide slits
240
7.13
The significance of the diffraction pattern
241
7.14
Another way of looking at
Лг
wide slits
246
Summary
250
Bibliography
253
8
Diffraction by a three-dimensional lattice
254
8.1
The diffraction pattern of a crystal
254
8.2
Non-normally incident waves
255
8.3
The diffraction pattern of a finite three-dimensional lattice
258
8.4
The diffraction pattern of an infinite lattice
260
8.5
The
Laue
equations
265
χ
Contents
8.6
The solution of the
Laue
equations
266
8.7
The reciprocal lattice
269
8.8
Reciprocal-lattice vectors and real-lattice planes
274
8.9
Bragg s law
277
8.10
The
Ewald
circle
278
8.11
The reciprocal lattice and diffraction
281
8.12
Why X-ray diffraction works
285
8.13
The
Ewald
sphere
286
8.14
The
Ewald
sphere and diffraction
288
8.15
Bragg s law and crystal planes
291
8.16
The effect of finite crystal size
293
Summary
294
9
The contents of the unit cell
297
9.1
The scattering of X-rays by a single electron
297
9.2
The scattering of X-rays by a distribution of electrons
300
9.3
The diffraction pattern of the motif
304
9.4
The calculation of the electron density function
307
9.5
Fourier synthesis
308
9.6
The calculation of structure factors
311
9.7
Atomic scattering factors
317
9.8
Anomalous scattering
322
9.9
Crystal symmetry and X-ray diffraction
323
9.10
Diffraction pattern symmetry
324
9.11
Friedeľs
law
326
9.12
The breakdown of
Friedeľs
law
328
9.13
Friedeľs
law and electron density calculations
331
9.14
Systematic absences
332
9.15
The determination of crystal symmetry
335
Summary
336
Review II
339
PART III STRUCTURE SOLUTION
10
Experimental techniques: sample preparation
343
10.1
Protein expression
343
10.2
Protein purification
347
10.3
Crystallisation
352
10.4
Crystal mounting
356
Summary
360
References
360
11
Experimental techniques: data collection and analysis
362
11.1
The origin of X-rays
362
11.2
Laboratory X-ray sources
363
11.3
Synchrotron sources
368
Contents
xî
11.4
Optimising the X-ray beam
370
11.5
The rotation method
375
11.6
Electronic detectors
378
11.7
Other aspects of data collection
381
11.8
Data processing
383
11.9
The basis of intensity data corrections
392
11.10
The polarisation factor
397
11.11
The
Lorentz
factor
398
11.12
Absorption
401
11.13
The temperature factor
405
11.14
Scaling and merging intensity measurements
413
11.15
Conversion of intensities to structure factor amplitudes
416
11.16
Normalised structure factors
418
11.17
Completeness of the data
419
11.18
Estimating the solvent content
420
11.19
Misindexing
and twinning
422
Summary
426
References
428
12
The phase problem and the Patterson function
431
12.1
The nature of the problem
431
12.2
Why is phase not detectable?
432
12.3
The Fourier transform of the intensities
433
12.4
The Patterson function and the crystal structure
434
12.5
The form of the Patterson function
437
12.6
The meaning of the Patterson function
438
12.7
Patterson maps
439
12.8
Patterson map symmetry
443
12.9
The use of Patterson maps
445
Summary
447
Bibliography
448
13
Molecular replacement
449
13.1
Solving the phase problem when the structure of a related
protein is known
449
13.2
The rotation function
451
13.3
Choice of variables in the rotation function
455
13.4
Testing the rotation function
460
13.5
Refining the rotation function solution
460
13.6
Symmetry of the rotation function
461
13.7
The translation function
461
13.8
Patterson-based translation methods
462
13.9
Reciprocal-space translation searches
464
13.10
Asymmetric unit of the translation function
467
13.11
Non-crystallographic symmetry
468
xii Contents
13.12
The packing function
470
13.13
Verifying the results
471
13.14
Wider applications of molecular replacement
472
Summary
473
References
473
14
Solving the phase problem experimentally
475
14.1
The techniques of solution
475
14.2
Isomorphism and the preparation of heavy-atom derivatives
476
14.3
Scaling and analysing derivative data
479
14.4
The difference Patterson function
483
14.5
The methods of Patterson solution
493
14.6
Direct methods for locating sites
496
14.7
Refinement of heavy-atom sites
505
14.8
Cross-phasing
507
14.9
The isomorphous replacement method
509
14.10
Exploiting anomalous scattering effects in phasing
519
14.11
Density modification
530
Summary
538
References
541
15
Refinement
545
15.1
The necessity for refinement
545
15.2
Obtaining the trial structure
548
15.3
Assessing the trial structure
551
15.4
Least-squares refinement
554
15.5
Theory of the least-squares method
555
15.6
The use of stereochemical restraints
565
15.7
The benefits of non-crystallographic symmetry
571
15.8
Modelling rigid-group displacement
572
15.9
Simulated annealing
572
15.10
Cross-validation
574
15.11
Use of Fourier maps in refinement
576
15.12
The difference Fourier synthesis
578
15.13
The maximum-likelihood method in refinement
586
15.14
Validation and deposition
587
Summary
589
References
591
16
Complementary diffraction methods
595
16.1
Finding hydrogen atoms in X-ray structures
595
16.2
Neutron protein crystallography
597
16.3
Neutron data collection
601
16.4
Neutron applications
604
16.5
Advantages of perdeuteration
606
16.6
X-ray
Laue
diffraction
607
Contents xiii
16.7 Laue
data processing
608
Summary
609
References
610
Review III
614
General bibliography
616
Index
617
|
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| id | DE-604.BV036581265 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:43:22Z |
| institution | BVB |
| isbn | 9780199559046 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-020502174 |
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| physical | XVII, 621 S. Ill., graph. Darst. |
| publishDate | 2011 |
| publishDateSearch | 2011 |
| publishDateSort | 2011 |
| publisher | Oxford Univ. Press |
| record_format | marc |
| spelling | Sherwood, Dennis Verfasser aut Crystals, X-rays and proteins comprehensive protein crystallography Dennis Sherwood ; Jon Cooper 1. publ. Oxford [u.a.] Oxford Univ. Press 2011 XVII, 621 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Proteine (DE-588)4076388-2 gnd rswk-swf Röntgenstrukturanalyse (DE-588)4137203-7 gnd rswk-swf Proteine (DE-588)4076388-2 s Röntgenstrukturanalyse (DE-588)4137203-7 s DE-604 Cooper, Jonathan M. Verfasser aut Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020502174&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Sherwood, Dennis Cooper, Jonathan M. Crystals, X-rays and proteins comprehensive protein crystallography Proteine (DE-588)4076388-2 gnd Röntgenstrukturanalyse (DE-588)4137203-7 gnd |
| subject_GND | (DE-588)4076388-2 (DE-588)4137203-7 |
| title | Crystals, X-rays and proteins comprehensive protein crystallography |
| title_auth | Crystals, X-rays and proteins comprehensive protein crystallography |
| title_exact_search | Crystals, X-rays and proteins comprehensive protein crystallography |
| title_full | Crystals, X-rays and proteins comprehensive protein crystallography Dennis Sherwood ; Jon Cooper |
| title_fullStr | Crystals, X-rays and proteins comprehensive protein crystallography Dennis Sherwood ; Jon Cooper |
| title_full_unstemmed | Crystals, X-rays and proteins comprehensive protein crystallography Dennis Sherwood ; Jon Cooper |
| title_short | Crystals, X-rays and proteins |
| title_sort | crystals x rays and proteins comprehensive protein crystallography |
| title_sub | comprehensive protein crystallography |
| topic | Proteine (DE-588)4076388-2 gnd Röntgenstrukturanalyse (DE-588)4137203-7 gnd |
| topic_facet | Proteine Röntgenstrukturanalyse |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020502174&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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