Principles of protein X-ray crystallography:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
New York, NY
Springer
2007
|
| Ausgabe: | 3. ed. |
| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | Hier auch später erschienene, unveränderte Nachdrucke |
| Beschreibung: | XIV, 332 S. Ill., graph. Darst. |
| ISBN: | 0387333347 9780387333342 0387337466 9780387337463 |
Internformat
MARC
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| 100 | 1 | |a Drenth, Jan |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Principles of protein X-ray crystallography |c Jan Drenth |
| 250 | |a 3. ed. | ||
| 264 | 1 | |a New York, NY |b Springer |c 2007 | |
| 300 | |a XIV, 332 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Hier auch später erschienene, unveränderte Nachdrucke | ||
| 650 | 4 | |a Proteine - Röntgenstrukturanalyse | |
| 650 | 4 | |a Proteins |x Analysis | |
| 650 | 4 | |a X-ray crystallography | |
| 650 | 0 | 7 | |a Röntgenstrukturanalyse |0 (DE-588)4137203-7 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Proteine |0 (DE-588)4076388-2 |2 gnd |9 rswk-swf |
| 689 | 0 | 0 | |a Proteine |0 (DE-588)4076388-2 |D s |
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-014833489 | ||
Datensatz im Suchindex
| _version_ | 1804135408651468800 |
|---|---|
| adam_text | Contents
Preface
to the Third Edition
v
Preface to the Second Edition
vi
Preface to the First Edition
vii
1
1
4
8
9
11
15
17
20
21
21
21
30
31
33
38
43
Chapter
1
Crystallizing a Protein
1.1
Introduction
1.2
Principles of Protein Crystallization
1.3
Crystallization Techniques
1.4
Crystallization of Lysozyme
1.5
A Preliminary Note on Crystals
1.6
Preparation for an X-ray Diffraction Experiment
1.7
Cryocooling
1.8
Notes
Summary
Chapter
2
X-ray Sources and Detectors
2.1
Introduction
2.2
X-ray Sources
2.3
Monochromators
2.4
Introduction to Cameras and Detectors
2.5
Detectors
2.6
The Rotation (Oscillation) Instrument
Summary
Contents xi
Chapter
3
Crystals
45
3.1
Introduction
45
3.2
Symmetry
49
3.3
Possible Symmetry for Protein Crystals
56
3.4
Coordinate Triplets: General and Special Positions
56
3.5
Asymmetric Unit
57
3.6
Point Groups
58
3.7
Crystal Systems
58
3.8
Radiation Damage
60
3.9
Characterization of the Crystals
61
Summary
63
Chapter
4
Theory of X-ray Diffraction by a Crystal
64
4.1
Introduction
64
4.2
Waves and Their Addition
65
4.3
A System of Two Electrons
68
4.4
Scattering by an Atom
71
4.5
Scattering by a Unit Cell
73
4.6
Scattering by a Crystal
74
4.7
Diffraction Conditions
76
4.8
Reciprocal Lattice and
Ewald
Construction
77
4.9
The Temperature Factor
81
4.10
Calculation of the Electron Density,
p (x y z)
84
4.11
Comparison of
FÍA*/)
and F(/ì£
fl
90
4.12
Symmetry in the Diffraction Pattern
91
4.13
Integral Reflection Conditions for Centered Lattices
95
4.14
Intensity Diffracted by a Crystal
96
4.15
Scattering by a Plane of Atoms
103
4.16
Choice of Wavelength, Size of Unit Cell, and Correction
of the Diffracted Intensity
105
Summary
107
Chapter
5
Average Reflection Intensity and Distribution of Structure
Factor Data
109
5.1
5.2
5.3
5.4
Chapter
6
Special Forms of the Structure Factor
119
Introduction
109
Average Intensity; Wilson Plots
111
The Distribution of Structure Factors
F
and Structure
Factor Amplitudes F
114
Crystal Twinning
116
Summary
118
x¡¡
Contents
6.1
Introduction
119
6.2
The Unitary Structure Factor
119
6.3
The Normalized Structure Factor
120
Summary
22
Chapter
7
The Solution of the Phase Problem by the Isomorphous
Replacement Method
123
7.1
Introduction
123
7.2
The Patterson Function
124
7.3
The Isomorphous Replacement Method
133
7.4
Effect of Heavy Atoms on X-ray Intensities
139
7.5
Determination of the Heavy Atom Parameters from
Centrosymmetric Projections
142
7.6
Parameters of Heavy Atoms Derived from Acentric
Reflections
144
7.7
The Difference Fourier Summation
146
7.8
Anomalous Scattering
148
7.9
The Anomalous Patterson Summation
152
7.10
One Common Origin for All Derivatives
154
7.11
Refinement of the Heavy Atom Parameters Using
Preliminary Protein Phase Angles
157
7.12
Protein Phase Angles
160
7.13
The Remaining Error in the Best Fourier Map
167
7.14
The Single Isomorphous Replacement Method
170
Summary
171
Chapter
8
Phase Improvement
172
8.1
Introduction
172
8.2
The OMIT Map With and Without Sim Weighting
173
8.3
Solvent Flattening
179
8.4
Noncrystallographic Symmetry and Molecular Averaging
185
8.5
Histogram Matching
187
8.6
wARP: Weighted Averaging of Multiple-Refined Dummy
Atomic Models
190
8.7
Further Considerations Concerning Density Modification
192
Summary
193
Chapter
9
Anomalous Scattering in the Determination of the
Protein Phase Angles and the Absolute Configuration
194
9.1
Introduction
194
9.2
Protein Phase Angle Determination with Anomalous Scattering
194
9.3
Improvement of Protein Phase Angles with
Anomalous Scattering
196
9.4
The Determination of the Absolute Configuration
198
9.5
Multiple- and Single-Wavelength Anomalous Diffraction
(MAD and SAD)
199
Summary
209
Contents xiii
Chapter
10
Molecular Replacement
210
10.1
Introduction
210
10.2
The Rotation Function
211
10.3
The Translation Function
217
Summary
230
Chapter
11
Direct Methods
231
11.1
Introduction
231
11.2
Shake-and-Bake
231
11.3
SHELXD
236
11.4
The Principle of Maximum Entropy
238
Summary
240
Chapter
12
Laue
Diffraction
241
12.1
Introduction
241
12.2
The Accessible Region of Reciprocal Space
242
12.3
The Multiple Problem
243
12.4
Unscrambling of Multiple Intensities
244
12.5
The Spatial Overlap Problem
245
12.6
Wavelength Normalization
245
Summary
246
Chapter
13
Refinement of the Model Structure
248
13.1
Introduction
248
13.2
The Mathematics of Refinement
251
13.3
The Principle of the Fast Fourier Transform Method
262
13.4
Specific Refinement Methods
264
Summary
278
Chapter
14
The Combination of Phase Information
279
14.1
Introduction
279
14.2
Phase Information from Isomorphous Replacement
280
14.3
Phase Information from Anomalous Scattering
282
14.4
Phase Information from Partial Structure Data,
Solvent Flattening, and Molecular Averaging
283
14.5
Phase Information from SAD
284
Summary
284
Chapter
15
Checking for Gross Errors and Estimating the Accuracy
of the Structural Model
285
15.1
Introduction
285
xiv
Contents
15.2
/ř-Factors
285
15.3
The Ramachandran Plot
287
15.4
Stereochemistry Check
287
15.5
The 3D-1D Profile Method
288
15.6
Quantitative Estimation of the Coordinate Error in the
Final Model
292
Summary
296
Chapter
16
Practical Protein Crystallization
297
16.1
Introduction
297
16.2
Gene Cloning and Expression
298
16.3
Protein Purification
299
16.4
Protein Crystallization
302
Summary
303
Appendix
1
A Compilation of Equations for Calculating Electron
Density Maps
305
Appendix
2
A Compilation of Reliability Indexes
308
Appendix
3
The Variation in the Intensity of X-ray Radiation
314
References
316
Index
326
|
| adam_txt |
Contents
Preface
to the Third Edition
v
Preface to the Second Edition
vi
Preface to the First Edition
vii
1
1
4
8
9
11
15
17
20
21
21
21
30
31
33
38
43
Chapter
1
Crystallizing a Protein
1.1
Introduction
1.2
Principles of Protein Crystallization
1.3
Crystallization Techniques
1.4
Crystallization of Lysozyme
1.5
A Preliminary Note on Crystals
1.6
Preparation for an X-ray Diffraction Experiment
1.7
Cryocooling
1.8
Notes
Summary
Chapter
2
X-ray Sources and Detectors
2.1
Introduction
2.2
X-ray Sources
2.3
Monochromators
2.4
Introduction to Cameras and Detectors
2.5
Detectors
2.6
The Rotation (Oscillation) Instrument
Summary
Contents xi
Chapter
3
Crystals
45
3.1
Introduction
45
3.2
Symmetry
49
3.3
Possible Symmetry for Protein Crystals
56
3.4
Coordinate Triplets: General and Special Positions
56
3.5
Asymmetric Unit
57
3.6
Point Groups
58
3.7
Crystal Systems
58
3.8
Radiation Damage
60
3.9
Characterization of the Crystals
61
Summary
63
Chapter
4
Theory of X-ray Diffraction by a Crystal
64
4.1
Introduction
64
4.2
Waves and Their Addition
65
4.3
A System of Two Electrons
68
4.4
Scattering by an Atom
71
4.5
Scattering by a Unit Cell
73
4.6
Scattering by a Crystal
74
4.7
Diffraction Conditions
76
4.8
Reciprocal Lattice and
Ewald
Construction
77
4.9
The Temperature Factor
81
4.10
Calculation of the Electron Density,
p (x y z)
84
4.11
Comparison of
FÍA*/)
and F(/ì£
fl
90
4.12
Symmetry in the Diffraction Pattern
91
4.13
Integral Reflection Conditions for Centered Lattices
95
4.14
Intensity Diffracted by a Crystal
96
4.15
Scattering by a Plane of Atoms
103
4.16
Choice of Wavelength, Size of Unit Cell, and Correction
of the Diffracted Intensity
105
Summary
107
Chapter
5
Average Reflection Intensity and Distribution of Structure
Factor Data
109
5.1
5.2
5.3
5.4
Chapter
6
Special Forms of the Structure Factor
119
Introduction
109
Average Intensity; Wilson Plots
111
The Distribution of Structure Factors
F
and Structure
Factor Amplitudes \F\
114
Crystal Twinning
116
Summary
118
x¡¡
Contents
6.1
Introduction
119
6.2
The Unitary Structure Factor
119
6.3
The Normalized Structure Factor
120
Summary
'22
Chapter
7
The Solution of the Phase Problem by the Isomorphous
Replacement Method
123
7.1
Introduction
123
7.2
The Patterson Function
124
7.3
The Isomorphous Replacement Method
133
7.4
Effect of Heavy Atoms on X-ray Intensities
139
7.5
Determination of the Heavy Atom Parameters from
Centrosymmetric Projections
142
7.6
Parameters of Heavy Atoms Derived from Acentric
Reflections
144
7.7
The Difference Fourier Summation
146
7.8
Anomalous Scattering
148
7.9
The Anomalous Patterson Summation
152
7.10
One Common Origin for All Derivatives
154
7.11
Refinement of the Heavy Atom Parameters Using
Preliminary Protein Phase Angles
157
7.12
Protein Phase Angles
160
7.13
The Remaining Error in the Best Fourier Map
167
7.14
The Single Isomorphous Replacement Method
170
Summary
171
Chapter
8
Phase Improvement
172
8.1
Introduction
172
8.2
The OMIT Map With and Without Sim Weighting
173
8.3
Solvent Flattening
179
8.4
Noncrystallographic Symmetry and Molecular Averaging
185
8.5
Histogram Matching
187
8.6
wARP: Weighted Averaging of Multiple-Refined Dummy
Atomic Models
190
8.7
Further Considerations Concerning Density Modification
192
Summary
193
Chapter
9
Anomalous Scattering in the Determination of the
Protein Phase Angles and the Absolute Configuration
194
9.1
Introduction
194
9.2
Protein Phase Angle Determination with Anomalous Scattering
194
9.3
Improvement of Protein Phase Angles with
Anomalous Scattering
196
9.4
The Determination of the Absolute Configuration
198
9.5
Multiple- and Single-Wavelength Anomalous Diffraction
(MAD and SAD)
199
Summary
209
Contents xiii
Chapter
10
Molecular Replacement
210
10.1
Introduction
210
10.2
The Rotation Function
211
10.3
The Translation Function
217
Summary
230
Chapter
11
Direct Methods
231
11.1
Introduction
231
11.2
Shake-and-Bake
231
11.3
SHELXD
236
11.4
The Principle of Maximum Entropy
238
Summary
240
Chapter
12
Laue
Diffraction
241
12.1
Introduction
241
12.2
The Accessible Region of Reciprocal Space
242
12.3
The Multiple Problem
243
12.4
Unscrambling of Multiple Intensities
244
12.5
The Spatial Overlap Problem
245
12.6
Wavelength Normalization
245
Summary
246
Chapter
13
Refinement of the Model Structure
248
13.1
Introduction
248
13.2
The Mathematics of Refinement
251
13.3
The Principle of the Fast Fourier Transform Method
262
13.4
Specific Refinement Methods
264
Summary
278
Chapter
14
The Combination of Phase Information
279
14.1
Introduction
279
14.2
Phase Information from Isomorphous Replacement
280
14.3
Phase Information from Anomalous Scattering
282
14.4
Phase Information from Partial Structure Data,
Solvent Flattening, and Molecular Averaging
283
14.5
Phase Information from SAD
284
Summary
284
Chapter
15
Checking for Gross Errors and Estimating the Accuracy
of the Structural Model
285
15.1
Introduction
285
xiv
Contents
15.2
/ř-Factors
285
15.3
The Ramachandran Plot
287
15.4
Stereochemistry Check
287
15.5
The 3D-1D Profile Method
288
15.6
Quantitative Estimation of the Coordinate Error in the
Final Model
292
Summary
296
Chapter
16
Practical Protein Crystallization
297
16.1
Introduction
297
16.2
Gene Cloning and Expression
298
16.3
Protein Purification
299
16.4
Protein Crystallization
302
Summary
303
Appendix
1
A Compilation of Equations for Calculating Electron
Density Maps
305
Appendix
2
A Compilation of Reliability Indexes
308
Appendix
3
The Variation in the Intensity of X-ray Radiation
314
References
316
Index
326 |
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| author | Drenth, Jan |
| author_facet | Drenth, Jan |
| author_role | aut |
| author_sort | Drenth, Jan |
| author_variant | j d jd |
| building | Verbundindex |
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| classification_rvk | WC 4170 WD 5100 WD 5275 |
| classification_tum | CHE 808f CHE 820f |
| ctrlnum | (OCoLC)255526188 (DE-599)BVBBV021618389 |
| dewey-full | 572.636 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.636 |
| dewey-search | 572.636 |
| dewey-sort | 3572.636 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Chemie |
| discipline_str_mv | Biologie Chemie |
| edition | 3. ed. |
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| id | DE-604.BV021618389 |
| illustrated | Illustrated |
| index_date | 2024-07-02T14:52:51Z |
| indexdate | 2024-07-09T20:40:02Z |
| institution | BVB |
| isbn | 0387333347 9780387333342 0387337466 9780387337463 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-014833489 |
| oclc_num | 255526188 |
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| owner | DE-20 DE-91G DE-BY-TUM DE-19 DE-BY-UBM DE-M49 DE-BY-TUM DE-703 DE-355 DE-BY-UBR |
| owner_facet | DE-20 DE-91G DE-BY-TUM DE-19 DE-BY-UBM DE-M49 DE-BY-TUM DE-703 DE-355 DE-BY-UBR |
| physical | XIV, 332 S. Ill., graph. Darst. |
| publishDate | 2007 |
| publishDateSearch | 2007 |
| publishDateSort | 2007 |
| publisher | Springer |
| record_format | marc |
| spelling | Drenth, Jan Verfasser aut Principles of protein X-ray crystallography Jan Drenth 3. ed. New York, NY Springer 2007 XIV, 332 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Hier auch später erschienene, unveränderte Nachdrucke Proteine - Röntgenstrukturanalyse Proteins Analysis X-ray crystallography Röntgenstrukturanalyse (DE-588)4137203-7 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf Proteine (DE-588)4076388-2 s Röntgenstrukturanalyse (DE-588)4137203-7 s DE-604 text/html http://deposit.dnb.de/cgi-bin/dokserv?id=2784092&prov=M&dok_var=1&dok_ext=htm Inhaltstext Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014833489&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Drenth, Jan Principles of protein X-ray crystallography Proteine - Röntgenstrukturanalyse Proteins Analysis X-ray crystallography Röntgenstrukturanalyse (DE-588)4137203-7 gnd Proteine (DE-588)4076388-2 gnd |
| subject_GND | (DE-588)4137203-7 (DE-588)4076388-2 |
| title | Principles of protein X-ray crystallography |
| title_auth | Principles of protein X-ray crystallography |
| title_exact_search | Principles of protein X-ray crystallography |
| title_exact_search_txtP | Principles of protein X-ray crystallography |
| title_full | Principles of protein X-ray crystallography Jan Drenth |
| title_fullStr | Principles of protein X-ray crystallography Jan Drenth |
| title_full_unstemmed | Principles of protein X-ray crystallography Jan Drenth |
| title_short | Principles of protein X-ray crystallography |
| title_sort | principles of protein x ray crystallography |
| topic | Proteine - Röntgenstrukturanalyse Proteins Analysis X-ray crystallography Röntgenstrukturanalyse (DE-588)4137203-7 gnd Proteine (DE-588)4076388-2 gnd |
| topic_facet | Proteine - Röntgenstrukturanalyse Proteins Analysis X-ray crystallography Röntgenstrukturanalyse Proteine |
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| work_keys_str_mv | AT drenthjan principlesofproteinxraycrystallography |