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Refinement at atomic resolution
International Tables for Crystallography (2012). Vol. F, ch. 18.4, pp. 485-498 [ doi:10.1107/97809553602060000858 ]
... to the apparent ADP () can be thought of as follows (Murshudov et al., 1999): where represents the fact that a crystal ... by maximum-likelihood procedures (Bricogne & Irwin, 1996; Pannu & Read, 1996; Murshudov et al., 1997). For small-molecule structures, accurate amplitude ... of B values for a protein structure, Micrococcus lysodecticus catalase (Murshudov et al., 1999), for two different crystals which diffracted ...
Relation to biological chemistry
International Tables for Crystallography (2012). Vol. F, Section 18.4.7, pp. 495-496 [ doi:10.1107/97809553602060000858 ]
Relation to biological chemistry 18.4.7. Relation to biological chemistry A question arises as to what biological issues are addressed by analysis of macromolecular structures at atomic resolution. For any protein, the overall structure of its fold, and hence its homology with other proteins, can already be provided by analyses at low ...
Quality assessment of the model
International Tables for Crystallography (2012). Vol. F, Section 18.4.6, p. 495 [ doi:10.1107/97809553602060000858 ]
... A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). The Cambridge Crystallographic Data Centre: computer-based search ...
Deformation density
International Tables for Crystallography (2012). Vol. F, Section 18.4.5.8, pp. 494-495 [ doi:10.1107/97809553602060000858 ]
Deformation density 18.4.5.8. Deformation density X-ray structures are generally modelled using the spherical-atom approximation for the scattering, which ignores the deviation from sphericity of the outer bonding and lone-pair electrons. Extensive studies over a long period have confirmed that the so-called deformation density, representing deviation from this ...
[more results from section 18.4.5 in volume F]
Validation of extra parameters during the refinement process
International Tables for Crystallography (2012). Vol. F, Section 18.4.4.4, p. 491 [ doi:10.1107/97809553602060000858 ]
Validation of extra parameters during the refinement process 18.4.4.4. Validation of extra parameters during the refinement process The introduction of additional parameters into the model always results in a reduction in the least-squares or maximum-likelihood residual - in crystallographic terms, the R factor. However, the statistical significance of this reduction ...
[more results from section 18.4.4 in volume F]
Computer power
International Tables for Crystallography (2012). Vol. F, Section 18.4.3.6, p. 489 [ doi:10.1107/97809553602060000858 ]
... the large size of the matrix, which increases as , where N is the number of parameters, means that for macromolecules with ...
[more results from section 18.4.3 in volume F]
Anisotropic scaling
International Tables for Crystallography (2012). Vol. F, Section 18.4.2.2, p. 488 [ doi:10.1107/97809553602060000858 ]
... several per cent in R and Rfree (Sheriff & Hendrickson, 1987; Murshudov et al., 1998). This ambiguity effectively disappears with use ... atomic ADPs. References Driessen, H., Haneef, M. I. J., Harris, G. W., Howlin, B., Khan, G. & Moss, D. S. (1989). RESTRAIN: restrained structure-factor ...
[more results from section 18.4.2 in volume F]
A theoretical approach to `atomic resolution'
International Tables for Crystallography (2012). Vol. F, Section 18.4.1.3, p. 487 [ doi:10.1107/97809553602060000858 ]
A theoretical approach to `atomic resolution' 18.4.1.3. A theoretical approach to `atomic resolution' An alternative and stricter definition of atomic resolution comes from using a measure of the information content of the data. There are a variety of definitions of the information in the data about the postulated model (see, for ...
[more results from section 18.4.1 in volume F]
Practical strategies
International Tables for Crystallography (2012). Vol. F, Section 18.4.8, p. 496 [ doi:10.1107/97809553602060000858 ]
... illustration. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA. Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S. & Dodson, ...
International Tables for Crystallography (2012). Vol. F, ch. 18.4, pp. 485-498 [ doi:10.1107/97809553602060000858 ]
... to the apparent ADP () can be thought of as follows (Murshudov et al., 1999): where represents the fact that a crystal ... by maximum-likelihood procedures (Bricogne & Irwin, 1996; Pannu & Read, 1996; Murshudov et al., 1997). For small-molecule structures, accurate amplitude ... of B values for a protein structure, Micrococcus lysodecticus catalase (Murshudov et al., 1999), for two different crystals which diffracted ...
Relation to biological chemistry
International Tables for Crystallography (2012). Vol. F, Section 18.4.7, pp. 495-496 [ doi:10.1107/97809553602060000858 ]
Relation to biological chemistry 18.4.7. Relation to biological chemistry A question arises as to what biological issues are addressed by analysis of macromolecular structures at atomic resolution. For any protein, the overall structure of its fold, and hence its homology with other proteins, can already be provided by analyses at low ...
Quality assessment of the model
International Tables for Crystallography (2012). Vol. F, Section 18.4.6, p. 495 [ doi:10.1107/97809553602060000858 ]
... A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). The Cambridge Crystallographic Data Centre: computer-based search ...
Deformation density
International Tables for Crystallography (2012). Vol. F, Section 18.4.5.8, pp. 494-495 [ doi:10.1107/97809553602060000858 ]
Deformation density 18.4.5.8. Deformation density X-ray structures are generally modelled using the spherical-atom approximation for the scattering, which ignores the deviation from sphericity of the outer bonding and lone-pair electrons. Extensive studies over a long period have confirmed that the so-called deformation density, representing deviation from this ...
[more results from section 18.4.5 in volume F]
Validation of extra parameters during the refinement process
International Tables for Crystallography (2012). Vol. F, Section 18.4.4.4, p. 491 [ doi:10.1107/97809553602060000858 ]
Validation of extra parameters during the refinement process 18.4.4.4. Validation of extra parameters during the refinement process The introduction of additional parameters into the model always results in a reduction in the least-squares or maximum-likelihood residual - in crystallographic terms, the R factor. However, the statistical significance of this reduction ...
[more results from section 18.4.4 in volume F]
Computer power
International Tables for Crystallography (2012). Vol. F, Section 18.4.3.6, p. 489 [ doi:10.1107/97809553602060000858 ]
... the large size of the matrix, which increases as , where N is the number of parameters, means that for macromolecules with ...
[more results from section 18.4.3 in volume F]
Anisotropic scaling
International Tables for Crystallography (2012). Vol. F, Section 18.4.2.2, p. 488 [ doi:10.1107/97809553602060000858 ]
... several per cent in R and Rfree (Sheriff & Hendrickson, 1987; Murshudov et al., 1998). This ambiguity effectively disappears with use ... atomic ADPs. References Driessen, H., Haneef, M. I. J., Harris, G. W., Howlin, B., Khan, G. & Moss, D. S. (1989). RESTRAIN: restrained structure-factor ...
[more results from section 18.4.2 in volume F]
A theoretical approach to `atomic resolution'
International Tables for Crystallography (2012). Vol. F, Section 18.4.1.3, p. 487 [ doi:10.1107/97809553602060000858 ]
A theoretical approach to `atomic resolution' 18.4.1.3. A theoretical approach to `atomic resolution' An alternative and stricter definition of atomic resolution comes from using a measure of the information content of the data. There are a variety of definitions of the information in the data about the postulated model (see, for ...
[more results from section 18.4.1 in volume F]
Practical strategies
International Tables for Crystallography (2012). Vol. F, Section 18.4.8, p. 496 [ doi:10.1107/97809553602060000858 ]
... illustration. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA. Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S. & Dodson, ...
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