Electron crystallography of biological macromolecules:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Oxford [u.a.]
Oxford Univ. Press
2007
|
| Schlagworte: | |
| Online-Zugang: | Table of contents only Publisher description Inhaltsverzeichnis |
| Beschreibung: | XV, 476 S. Ill., graph. Darst. |
| ISBN: | 0195088719 9780195088717 |
Internformat
MARC
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| 245 | 1 | 0 | |a Electron crystallography of biological macromolecules |c Robert M. Glaeser ... |
| 264 | 1 | |a Oxford [u.a.] |b Oxford Univ. Press |c 2007 | |
| 300 | |a XV, 476 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 4 | |a Crystallography | |
| 650 | 4 | |a Electron microscopy | |
| 650 | 4 | |a Macromolecules | |
| 650 | 0 | 7 | |a Kristallstrukturanalyse |0 (DE-588)4137204-9 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Kristallographie |0 (DE-588)4033217-2 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Biopolymere |0 (DE-588)4006893-6 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Elektronenmikroskopie |0 (DE-588)4014327-2 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Elektronenbeugung |0 (DE-588)4151862-7 |2 gnd |9 rswk-swf |
| 689 | 0 | 0 | |a Biopolymere |0 (DE-588)4006893-6 |D s |
| 689 | 0 | 1 | |a Kristallographie |0 (DE-588)4033217-2 |D s |
| 689 | 0 | 2 | |a Elektronenmikroskopie |0 (DE-588)4014327-2 |D s |
| 689 | 0 | |5 DE-604 | |
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| 689 | 1 | |C b |5 DE-604 | |
| 700 | 1 | |a Glaeser, Robert M. |d 1934- |e Sonstige |0 (DE-588)1237857880 |4 oth | |
| 856 | 4 | |u http://www.loc.gov/catdir/toc/ecip0614/2006017707.html |3 Table of contents only | |
| 856 | 4 | |u http://www.loc.gov/catdir/enhancements/fy0723/2006017707-d.html |3 Publisher description | |
| 856 | 4 | 2 | |m Digitalisierung UB Regensburg - ADAM Catalogue Enrichment |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016068756&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-016068756 | ||
Datensatz im Suchindex
| _version_ | 1804137118635655168 |
|---|---|
| adam_text | Contents
1
INTRODUCTION
3
1.
1
El
ее
imn
crystallography provides access to a unique class of problems in
structural molecular biology
3
1.2
High-resolution crystallography requires averaging of structures that are
present in multiple copies
5
1.3
Electron crystallography can produce three-dimensional density maps that
are
interpretable
in terms of an atomic model of the structure
7
1.4
Electron crystallography has developed from rich intellectual origins in
optics, electron microscopy, and x-ray crystallography 1
1
1
.5
Objectives of this book
15
2
STRUCTURE DETERMINATION AS IT HAS BEEN DEVELOPED THROUGH
X-RAY CRYSTALLOGRAPHY
1 7
2.1
Introduction
17
2.2
Structure analysis by x-ray crystallography requires well-ordered,
three-dimensional
сіл
stals
18
2.3
The practical steps of data collection and data analysis have become
very
efficiënt
19
2.4
The Founer transform plays a central role in understanding the analysis
of diffraction data
19
2.5
The Fourier transform of a crystal represents discrete, regular samples
of the continuous Fourier transform of the molecule
26
ix
Contents
2.6
The disorder that exists
m
real crystals can result in easily observed
changes in the Fourier transform.
32
2.7
The
Ewald
sphere: a powerful mental picture that shows what part
of the Fourier transform can be measured for every
orientation
of the specimen
34
2.8
Bragg s taw relates the measured scattering angle to the size of the
repeat-distance for each sinusoidal term in the Fourier transform
of the object
36
2.9
information about the relative phase of each sinusoidal term, is lost in
diffraction patterns
38
2.10
The crystallograpbic phase problem is usually solved by using additional
data obtained from heavy-atom derivatives of the original molecular
crystals
39
2.11
The three-dimensional electron density of the molecule can be calculated
from the experimentally measured amplitudes and phases of the Fourier
transform
43
2.12
The
3-D
density map must be interpreted in terms of other available
information, to provide a model of the structure
44
2.13
A more accurate
estimare
of the structure can be obtained by further
refinement of the model
46
2.14
Published structures are made available through a public-domain
database
48
FOURIER OPTICS AND THE ROLE OF DIFFRACTION IN IMAGE
FORMATION
49
3.1
Introduction
49
3.2
Abbe s diffraction theory of images: image formation is the
two-dimensional equivalent of the crystallographer s inverse
Fourier transform
50
3.3
Zermke and the invention of phase contrast microscopy
52
3.4
The rigorous diffraction theory of image formation describes images
in terms of the inverse Fourier transform
54
3.5
The lens as a linear system: transfer functions play an important role
in Fourier optics
59
3.6
The most common applications of Fourier optics
m
electron, crystallography
require that the specimen behaves like a weak phase object
63
3.7
The image intensity for a weak phase object remains linear in the projected
Coulomb potential
64
3.8
The concept of a phase contrast transfer function is of central importance
in the interpretation of high-resolution images
67
3.9
Partial coherence imposes an envelope on the phase contrast transfer
function
69
3.10
Amplitude contrast can also contribute in an important way to images
of thin, biological specimens
72
3.11
Single side band images: blocking half of the diffraction pattern
produces images whose transfer function has unit gain at all spatial
frequencies
74
Contents xi
3.12
Tilted illumination produces images for which the transfer function
includes both phase errors and amplitude modulations
75
3.13
Summary: Fourier optics is an important part of the
conceptual
foundation of electron crystallography
76
THEORETICAL FOUNDATIONS SPECIFIC TO ELECTRON
CRYSTALLOGRAPHY
77
4.1
Introduction
77
4.2
The single-scattering (kinematic scattering) approximation and
the weak phase object approximation are mathematically similar
but not identical
78
4.3
Proof of the projection theorem
81
4.4
Two important simplifications of crystallographic structure analysis occur
when the specimen is approximated as a weak phase object
82
4.5
Three-dimensional Fourier space is sampled by collecting data at many
different tilt angles
83
4.6
The resolution of a
3-D
reconstruction is determined by the spatial
frequency limit of the measurements and by the completeness
of
3-D
data collection
85
4.7
Radiation damage represents a much more important experimental constraint
m
electron crystallography than in
х
-ray crystallography
93
4.8
Images become very noisy at high resolution due to the finite,
low exposures which are permitted within acceptable limits
of radiation damage
101
4.9
Spatial averaging must be used in order to overcome the limited
statistical definition that is possible when images are recorded
with safe levels of electron exposure
102
4.10
The. amount of averaging required is determined by the number of
scattered electrons and by the image quality
104
INSTRUMENTATION AND EXPERIMENTAL TECHNIQUES
1 06
5.1
Introduction
106
5.2
The basic design of an electron microscope is much like that of a light
microscope
107
5.3
Technical features that are specific to electron optics
108
5.4
Specimen stages
123
5.5
Detectors that are suitable for observing and recording images and
diffraction patterns
126
5.6
Low-dose techniques make it possible to record high-resolution
images and diffraction patterns even from easily damaged
specimens
131
5.7
Spot-scan imaging can minimize beam-induced movement
134
5.8
Samples prepared as self-supported specimens within (or over)
holes require additional precautions in order to minimize
specimen charging
137
xii Contents
6
SPECIMEN
PREPARATION
139
6.1
Introduction
139
6.2
Negative staining provides high contrast as well as excellent stability in the
electron beam
140
6.3
Metal shadowing produces stable samples which reveal surface
topography
142
6.4
Glucose and other sustains can preserve macromolecular structures
to high resolution.
145
6.5
Contrast matching can be manipulated by using embedding media
with different densities
147
6.6
Embedding in vitreous ice is the preferred alternative for the preparation
of unstained, hydrated specimens
150
6.7
Charging and mechanical stability vary with details of the specimen
preparation method
159
6.8
Preparing extremely flat specimens continues to be one of the most important
challenges when working with 2-D crystals
161
7
SYMMETRY AND ORDER IN TWO DIMENSIONS
167
7.1
Introduction
167
7.2
Classes of symmetry in projection
168
7.3
Three-dimensional symmetry classes for monolayer crystals
175
7.4
The Fourier transform of a 2-D crystal is sampled at discrete points
in two dimensions, but it is continuous i.n the third dimension.
182
7.5
Disorder and crystalline defects are an
important
fact of life
187
8
TWO-DIMENSIONAL CRYSTALLIZATION TECHNIQUES
194
8.1
Introduction
194
8.2
Integra] membrane proteins represent a natural target for
2-D crystallization
195
8.3
Many soluble proteins also form very thin crystals
201
8.4
Crystallization at interfaces has potential for wide generality
203
9
DATA PROCESSING: DIFFRACTION PATTERNS OF
2-D CRYSTALS
21 1
9.1
Introduction
211
9.2
Diffraction intensities are used in a variety of ways in electron
crystallography
212
9.3
Data that have been recorded on photographic film must be converted to
digital form with a scanning microdensitometer
213
9.4
Density versus exposure characteristics can be used to convert the film
density to the corresponding value of electron intensity
215
9.5
Data can also be collected by direct electronic readout rather than on
photographic film
217
9.6
The digitized diffraction patterns are then indexed and reduced to the
final diffraction intensities
219
Contents xiii
9.7
Intensities from individual diffraction patterns are merged to form
a
3-D
data set
225
9.8
Factors that affect data quality
230
10
DATA PROCESSING: IMAGES OF 2-D CRYSTALS
234
10.1
Introduction
234
10.2
Optical diffraction is an effective tool for the preliminary evaluation of
image quality
235
10.3
Conversion of the image to a digital form is necessary for computer
processing
237
10.4
The fast Fourier transform is an efficient algorithm for numerical
computation
244
10.5
Images of crystals: indexing the Fourier transform is similar to indexing
the electron diffraction pattern
246
10.6
Extraction of amplitudes and phases from the indexed Fourier
transform
247
10.7
Establishing a common phase origin allows data from separate crystals
to be merged into a
3-D
data set
253
10.8
Evaluation of data quality is based on the signal-to-noise ratio
257
10.9
Quasi-optical filtering reduces the noise in the image
259
10.10
Correction for distortions in the image increases the signal quality
263
10.11
Corrections are also required for other systematic image defects
270
11
HIGH-RESOLUTION DENSITY MAPS AND THEIR STRUCTURAL
INTERPRETATION
277
11.1
Introduction
277
11.2
Three-dimensional density maps are computed from discrete samples
of the complex structure factors
278
11.3
Options for the display of
3-D
density maps
279
11.4
The missing cone of data results in poorer resolution in the direction
perpendicular to the plane of the 2-D crystal
282
11.5
Interpretation of the high-resolution map involves building the known
chemical structure into the
3-D
density
288
11.6
Accurate atomic-resolution models can also be obtained by docking
atomic models of individual components into the
3-D
density map
of a macromolecular complex
291
11.7
Refinement of an atomic-resolution model may proceed in a different
way for electron crystallography than is.traditionally done in x-ray
crystallography
293
11.8
Difference Fourier maps
300
12
ELECTRON CRYSTALLOGRAPHY OF HELICAL STRUCTURES
304
12.1
Introduction
304
12.2
Ideal helices and their diffraction patterns
307
12.3
Real helices and their diffraction patterns
318
ІЗ
•Ί
..ζ
13
.3
13
.4
13.5
13
.6
13
.7
13
.8
13
.9
13
.10
13
.11
xiv Contents
12.4
The hardest step: indexing the diffraction pattern
325
12.5
Gathering amplitudes and phases is the next step in the reconstruction
process
330
12.6
Calculating and interpreting three-dimensional maps
336
12.7
Helical particles with a seam can be analyzed by extending the method
for helical particles
339
12.8
Helical structures can be analyzed using single-particle methods
340
12.9
The future looks bright
342
13
ICOSAHEDRAL PARTICLES
343
13.1
Introduction
343
Description of an icosahedron
344
Local symmetries can be present within an asymmetric unit
347
Theory of icosahedral reconstruction
347
Experimental considerations
349
Data evaluation
351
Image restoration
352
Initial model building and structure refinement
354
Resolution evaluation
360
Poststructure
analysis
362
Atomic model determination
363
14
SINGLE PARTICLES
365
14.1
Introduction
365
14.2
A certam
minimum dose is required to align images of single
molecules
368
14.3
Due to the lack of symmetries,
3-D
imaging requires coverage of the
·
entire angular space
369
14.4
Conformational variability increases the total number of images needed
to achieve higheT resolution
370
14.5
Alignment of particles is required for averaging and image reconstruction,
and its principal tool is the cross-correlation function
371
14.6
Classification may be used to divide the projection set according to
viewing directions, conformations, and Hgand-binding states
374
14.7
Vanational patterns among images of macromolecules can be found by
using multivariate data analysis or self-organized maps
375
14.8
Two useful methods of classification in single particle analysis are
hierarchical ascendant classification and
К
-means clustering
385
14.9
Real-space reconstruction techniques can deal with the general
3-D
projection geometries encountered in single-particle reconstruction
388
14.10
Random-conical and common-lines methods can provide angular
relationships among the molecule projections, as a way to jump-start
a reconstruction project
395
14.11
Angular refinement methods are used to proceed from the initial
reconstruction to the final reconstruction
399
14.12
Single-particle reconstruction in practice
401
14.13
What are the prospects of achieving atomic resolution?
413
Contents xv
15 SPECIAL
CONSIDERATIONS
ENCOUNTERED WITH
THICK SPECIMENS
415
15.1
Introduction
415
15.2
Dynamical diffraction can be described by a number of different,
but equivalent mathematical formalisms
416
15.3
Conditions when kinematic diffraction theory fails
419
15.4
Strong dynamical diffraction effects need not interfere with subsequent
refinement of an atomic-resolution model of the structure
424
15.5
Fresnel diffraction alone can become significant in thick specimens
426
15.6
Curvature of the
Ewald
sphere destroys the appearance of
Friede!
symmetry at high resolution and at high tilt angles
428
15.7
Inelastic scattering becomes an important consideration in
thick specimens
430
15.8
A final caution: failure of
Friede]
symmetry for thick specimens
can be due to curvature of the
Ewald
sphere, dynamical diffraction,
or inelastic scattering
437
References
441
Index
469
|
| adam_txt |
Contents
1
INTRODUCTION
3
1.
1
El
ее
imn
crystallography provides access to a unique class of problems in
structural molecular biology
3
1.2
High-resolution crystallography requires averaging of structures that are
present in multiple copies
5
1.3
Electron crystallography can produce three-dimensional density maps that
are
interpretable
in terms of an atomic model of the structure
7
1.4
Electron crystallography has developed from rich intellectual origins in
optics, electron microscopy, and x-ray crystallography 1
1
1
.5
Objectives of this book
15
2
STRUCTURE DETERMINATION AS IT HAS BEEN DEVELOPED THROUGH
X-RAY CRYSTALLOGRAPHY
1 7
2.1
Introduction
17
2.2
Structure analysis by x-ray crystallography requires well-ordered,
three-dimensional
сіл
stals
18
2.3
The practical steps of data collection and data analysis have become
very
efficiënt
19
2.4
The Founer transform plays a central role in understanding the analysis
of diffraction data
19
2.5
The Fourier transform of a crystal represents discrete, regular samples
of the continuous Fourier transform of the molecule
26
ix
Contents
2.6
The disorder that exists
m
real crystals can result in easily observed
changes in the Fourier transform.
32
2.7
The
Ewald
sphere: a powerful mental picture that shows what part
of the Fourier transform can be measured for every
orientation
of the specimen
34
2.8
Bragg\s taw relates the measured scattering angle to the size of the
repeat-distance for each sinusoidal term in the Fourier transform
of the object
36
2.9
information about the relative phase of each sinusoidal term, is lost in
diffraction patterns
38
2.10
The crystallograpbic phase problem is usually solved by using additional
data obtained from heavy-atom derivatives of the original molecular
crystals
39
2.11
The three-dimensional electron density of the molecule can be calculated
from the experimentally measured amplitudes and phases of the Fourier
transform
43
2.12
The
3-D
density map must be interpreted in terms of other available
information, to provide a model of the structure
44
2.13
A more accurate
estimare
of the structure can be obtained by further
refinement of the model
46
2.14
Published structures are made available through a public-domain
database
48
FOURIER OPTICS AND THE ROLE OF DIFFRACTION IN IMAGE
FORMATION
49
3.1
Introduction
49
3.2
Abbe's diffraction theory of images: image formation is the
two-dimensional equivalent of the crystallographer's "inverse
Fourier transform"
50
3.3
Zermke and the invention of phase contrast microscopy
52
3.4
The rigorous diffraction theory of image formation describes images
in terms of the inverse Fourier transform
54
3.5
The lens as a linear system: transfer functions play an important role
in Fourier optics
59
3.6
The most common applications of Fourier optics
m
electron, crystallography
require that the specimen behaves like a weak phase object
63
3.7
The image intensity for a weak phase object remains linear in the projected
Coulomb potential
64
3.8
The concept of a "phase contrast transfer function" is of central importance
in the interpretation of high-resolution images
67
3.9
Partial coherence imposes an envelope on the phase contrast transfer
function
69
3.10
Amplitude contrast can also contribute in an important way to images
of thin, biological specimens
72
3.11
Single side band images: blocking half of the diffraction pattern
produces images whose transfer function has unit gain at all spatial
frequencies
74
Contents xi
3.12
Tilted illumination produces images for which the transfer function
includes both phase errors and amplitude modulations
75
3.13
Summary: Fourier optics is an important part of the
conceptual
foundation of electron crystallography
76
THEORETICAL FOUNDATIONS SPECIFIC TO ELECTRON
CRYSTALLOGRAPHY
77
4.1
Introduction
77
4.2
The single-scattering (kinematic scattering) approximation and
the weak phase object approximation are mathematically similar
but not identical
78
4.3
Proof of the projection theorem
81
4.4
Two important simplifications of crystallographic structure analysis occur
when the specimen is approximated as a weak phase object
82
4.5
Three-dimensional Fourier space is sampled by collecting data at many
different tilt angles
83
4.6
The resolution of a
3-D
reconstruction is determined by the spatial
frequency limit of the measurements and by the completeness
of
3-D
data collection
85
4.7
Radiation damage represents a much more important experimental constraint
m
electron crystallography than in
х
-ray crystallography
93
4.8
Images become very noisy at high resolution due to the finite,
"low" exposures which are permitted within acceptable limits
of radiation damage
101
4.9
Spatial averaging must be used in order to overcome the limited
statistical definition that is possible when images are recorded
with "safe" levels of electron exposure
102
4.10
The. amount of averaging required is determined by the number of
scattered electrons and by the image quality
104
INSTRUMENTATION AND EXPERIMENTAL TECHNIQUES
1 06
5.1
Introduction
106
5.2
The basic design of an electron microscope is much like that of a light
microscope
107
5.3
Technical features that are specific to electron optics
108
5.4
Specimen stages
123
5.5
Detectors that are suitable for observing and recording images and
diffraction patterns
126
5.6
Low-dose techniques make it possible to record high-resolution
images and diffraction patterns even from easily damaged
specimens
131
5.7
Spot-scan imaging can minimize beam-induced movement
134
5.8
Samples prepared as self-supported specimens within (or over)
holes require additional precautions in order to minimize
specimen charging
137
xii Contents
6
SPECIMEN
PREPARATION
139
6.1
Introduction
139
6.2
Negative staining provides high contrast as well as excellent stability in the
electron beam
140
6.3
Metal shadowing produces stable samples which reveal surface
topography
142
6.4
Glucose and other "sustains" can preserve macromolecular structures
to high resolution.
145
6.5
Contrast matching can be manipulated by using embedding media
with different densities
147
6.6
Embedding in vitreous ice is the preferred alternative for the preparation
of unstained, hydrated specimens
150
6.7
Charging and mechanical stability vary with details of the specimen
preparation method
159
6.8
Preparing extremely flat specimens continues to be one of the most important
challenges when working with 2-D crystals
161
7
SYMMETRY AND ORDER IN TWO DIMENSIONS
167
7.1
Introduction
167
7.2
Classes of symmetry in projection
168
7.3
Three-dimensional symmetry classes for monolayer crystals
175
7.4
The Fourier transform of a 2-D crystal is sampled at discrete points
in two dimensions, but it is continuous i.n the third dimension.
182
7.5
Disorder and crystalline defects are an
important
fact of life
187
8
TWO-DIMENSIONAL CRYSTALLIZATION TECHNIQUES
194
8.1
Introduction
194
8.2
Integra] membrane proteins represent a natural target for
2-D crystallization
195
8.3
Many soluble proteins also form very thin crystals
201
8.4
Crystallization at interfaces has potential for wide generality
203
9
DATA PROCESSING: DIFFRACTION PATTERNS OF
2-D CRYSTALS
21 1
9.1
Introduction
211
9.2
Diffraction intensities are used in a variety of ways in electron
crystallography
212
9.3
Data that have been recorded on photographic film must be converted to
digital form with a scanning microdensitometer
213
9.4
Density versus exposure characteristics can be used to convert the film
density to the corresponding value of electron intensity
215
9.5
Data can also be collected by direct electronic readout rather than on
photographic film
217
9.6
The digitized diffraction patterns are then indexed and reduced to the
final diffraction intensities
219
Contents xiii
9.7
Intensities from individual diffraction patterns are merged to form
a
3-D
data set
225
9.8
Factors that affect data quality
230
10
DATA PROCESSING: IMAGES OF 2-D CRYSTALS
234
10.1
Introduction
234
10.2
Optical diffraction is an effective tool for the preliminary evaluation of
image quality
235
10.3
Conversion of the image to a digital form is necessary for computer
processing
237
10.4
The fast Fourier transform is an efficient algorithm for numerical
computation
244
10.5
Images of crystals: indexing the Fourier transform is similar to indexing
the electron diffraction pattern
246
10.6
Extraction of amplitudes and phases from the indexed Fourier
transform
247
10.7
Establishing a common phase origin allows data from separate crystals
to be merged into a
3-D
data set
253
10.8
Evaluation of data quality is based on the signal-to-noise ratio
257
10.9
Quasi-optical filtering reduces the noise in the image
259
10.10
Correction for distortions in the image increases the signal quality
263
10.11
Corrections are also required for other systematic image defects
270
11
HIGH-RESOLUTION DENSITY MAPS AND THEIR STRUCTURAL
INTERPRETATION
277
11.1
Introduction
277
11.2
Three-dimensional density maps are computed from discrete samples
of the complex structure factors
278
11.3
Options for the display of
3-D
density maps
279
11.4
The missing cone of data results in poorer resolution in the direction
perpendicular to the plane of the 2-D crystal
282
11.5
Interpretation of the high-resolution map involves building the known
chemical structure into the
3-D
density
288
11.6
Accurate atomic-resolution models can also be obtained by docking
atomic models of individual components into the
3-D
density map
of a macromolecular complex
291
11.7
Refinement of an atomic-resolution model may proceed in a different
way for electron crystallography than is.traditionally done in x-ray
crystallography
293
11.8
Difference Fourier maps
300
12
ELECTRON CRYSTALLOGRAPHY OF HELICAL STRUCTURES
304
12.1
Introduction
304
12.2
Ideal helices and their diffraction patterns
307
12.3
Real helices and their diffraction patterns
318
ІЗ
•Ί
.ζ
13
.3
13
.4
13.5
13
.6
13
.7
13
.8
13
.9
13
.10
13
.11
xiv Contents
12.4
The hardest step: indexing the diffraction pattern
325
12.5
Gathering amplitudes and phases is the next step in the reconstruction
process
330
12.6
Calculating and interpreting three-dimensional maps
336
12.7
Helical particles with a seam can be analyzed by extending the method
for helical particles
339
12.8
Helical structures can be analyzed using single-particle methods
340
12.9
The future looks bright
342
13
ICOSAHEDRAL PARTICLES
343
13.1
Introduction
343
Description of an icosahedron
344
Local symmetries can be present within an asymmetric unit
347
Theory of icosahedral reconstruction
347
Experimental considerations
349
Data evaluation
351
Image restoration
352
Initial model building and structure refinement
354
Resolution evaluation
360
Poststructure
analysis
362
Atomic model determination
363
14
SINGLE PARTICLES
365
14.1
Introduction
365
14.2
A certam
minimum dose is required to align images of single
molecules
368
14.3
Due to the lack of symmetries,
3-D
imaging requires coverage of the
·
entire angular space
369
14.4
Conformational variability increases the total number of images needed
to achieve higheT resolution
370
14.5
Alignment of particles is required for averaging and image reconstruction,
and its principal tool is the cross-correlation function
371
14.6
Classification may be used to divide the projection set according to
viewing directions, conformations, and Hgand-binding states
374
14.7
Vanational patterns among images of macromolecules can be found by
using multivariate data analysis or self-organized maps
375
14.8
Two useful methods of classification in single particle analysis are
hierarchical ascendant classification and
К
-means clustering
385
14.9
Real-space reconstruction techniques can deal with the general
3-D
projection geometries encountered in single-particle reconstruction
388
14.10
Random-conical and common-lines methods can provide angular
relationships among the molecule projections, as a way to jump-start
a reconstruction project
395
14.11
Angular refinement methods are used to proceed from the initial
reconstruction to the final reconstruction
399
14.12
Single-particle reconstruction in practice
401
14.13
What are the prospects of achieving atomic resolution?
413
Contents xv
15 SPECIAL
CONSIDERATIONS
ENCOUNTERED WITH
THICK SPECIMENS
415
15.1
Introduction
415
15.2
Dynamical diffraction can be described by a number of different,
but equivalent mathematical formalisms
416
15.3
Conditions when kinematic diffraction theory fails
419
15.4
Strong dynamical diffraction effects need not interfere with subsequent
refinement of an atomic-resolution model of the structure
424
15.5
Fresnel diffraction alone can become significant in thick specimens
426
15.6
Curvature of the
Ewald
sphere destroys the appearance of
Friede!
symmetry at high resolution and at high tilt angles
428
15.7
Inelastic scattering becomes an important consideration in
thick specimens
430
15.8
A final caution: failure of
Friede]
symmetry for thick specimens
can be due to curvature of the
Ewald
sphere, dynamical diffraction,
or inelastic scattering
437
References
441
Index
469 |
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| callnumber-first | Q - Science |
| callnumber-label | QD906 |
| callnumber-raw | QD906.7.E37 |
| callnumber-search | QD906.7.E37 |
| callnumber-sort | QD 3906.7 E37 |
| callnumber-subject | QD - Chemistry |
| classification_rvk | WC 2700 WC 3100 WD 5100 |
| classification_tum | CHE 808f GEO 424f CHE 264f |
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| dewey-search | 547/.704425 |
| dewey-sort | 3547 6704425 |
| dewey-tens | 540 - Chemistry and allied sciences |
| discipline | Chemie / Pharmazie Geowissenschaften Biologie Chemie |
| discipline_str_mv | Chemie / Pharmazie Geowissenschaften Biologie Chemie |
| format | Book |
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| illustrated | Illustrated |
| index_date | 2024-07-02T18:44:37Z |
| indexdate | 2024-07-09T21:07:13Z |
| institution | BVB |
| isbn | 0195088719 9780195088717 |
| language | English |
| lccn | 2006017707 |
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| physical | XV, 476 S. Ill., graph. Darst. |
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| spelling | Electron crystallography of biological macromolecules Robert M. Glaeser ... Oxford [u.a.] Oxford Univ. Press 2007 XV, 476 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Crystallography Electron microscopy Macromolecules Kristallstrukturanalyse (DE-588)4137204-9 gnd rswk-swf Kristallographie (DE-588)4033217-2 gnd rswk-swf Biopolymere (DE-588)4006893-6 gnd rswk-swf Elektronenmikroskopie (DE-588)4014327-2 gnd rswk-swf Elektronenbeugung (DE-588)4151862-7 gnd rswk-swf Biopolymere (DE-588)4006893-6 s Kristallographie (DE-588)4033217-2 s Elektronenmikroskopie (DE-588)4014327-2 s DE-604 Kristallstrukturanalyse (DE-588)4137204-9 s Elektronenbeugung (DE-588)4151862-7 s b DE-604 Glaeser, Robert M. 1934- Sonstige (DE-588)1237857880 oth http://www.loc.gov/catdir/toc/ecip0614/2006017707.html Table of contents only http://www.loc.gov/catdir/enhancements/fy0723/2006017707-d.html Publisher description 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=016068756&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Electron crystallography of biological macromolecules Crystallography Electron microscopy Macromolecules Kristallstrukturanalyse (DE-588)4137204-9 gnd Kristallographie (DE-588)4033217-2 gnd Biopolymere (DE-588)4006893-6 gnd Elektronenmikroskopie (DE-588)4014327-2 gnd Elektronenbeugung (DE-588)4151862-7 gnd |
| subject_GND | (DE-588)4137204-9 (DE-588)4033217-2 (DE-588)4006893-6 (DE-588)4014327-2 (DE-588)4151862-7 |
| title | Electron crystallography of biological macromolecules |
| title_auth | Electron crystallography of biological macromolecules |
| title_exact_search | Electron crystallography of biological macromolecules |
| title_exact_search_txtP | Electron crystallography of biological macromolecules |
| title_full | Electron crystallography of biological macromolecules Robert M. Glaeser ... |
| title_fullStr | Electron crystallography of biological macromolecules Robert M. Glaeser ... |
| title_full_unstemmed | Electron crystallography of biological macromolecules Robert M. Glaeser ... |
| title_short | Electron crystallography of biological macromolecules |
| title_sort | electron crystallography of biological macromolecules |
| topic | Crystallography Electron microscopy Macromolecules Kristallstrukturanalyse (DE-588)4137204-9 gnd Kristallographie (DE-588)4033217-2 gnd Biopolymere (DE-588)4006893-6 gnd Elektronenmikroskopie (DE-588)4014327-2 gnd Elektronenbeugung (DE-588)4151862-7 gnd |
| topic_facet | Crystallography Electron microscopy Macromolecules Kristallstrukturanalyse Kristallographie Biopolymere Elektronenmikroskopie Elektronenbeugung |
| url | http://www.loc.gov/catdir/toc/ecip0614/2006017707.html http://www.loc.gov/catdir/enhancements/fy0723/2006017707-d.html http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016068756&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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