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Bonds and angles
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3, pp. 477-481 [ doi:10.1107/97809553602060000857 ]
... amino-acid side chains EH denotes the values of Engh & Huber (1991), which were clustered according to atom type. The EH99 ... CH2 as CA, required new atom-type definitions for Engh & Huber (EH) (1991) parameterization to account for parameter-average differences of ... angles (°) of peptide backbone fragments EH denotes parameters from Engh & Huber (1991). Bold values mark important updates for angles ...
[more results from section 18.3.2 in volume F]
Risk of restraints: bias, lack of cross validation
International Tables for Crystallography (2012). Vol. F, Section 18.3.1.2, p. 474 [ doi:10.1107/97809553602060000857 ]
... preferentially chosen in model building, exaggerating their frequency. References Hooft, R. W. W., Sander, C. & Vriend, G. (1997). Objectively judging ...
[more results from section 18.3.1 in volume F]
Structure quality and target parameters
International Tables for Crystallography (2012). Vol. F, ch. 18.3, pp. 474-484 [ doi:10.1107/97809553602060000857 ]
... the CSD have come into widespread use for protein (Engh & Huber, 1991; Brünger, 1993; Priestle, 1994) and nucleic acid (Parkinson ... amino-acid side chains EH denotes the values of Engh & Huber (1991), which were clustered according to atom type. The EH99 ... CH2 as CA, required new atom-type definitions for Engh & Huber (EH) (1991) parameterization to account for parameter-average differences ...
Future perspectives
International Tables for Crystallography (2012). Vol. F, Section 18.3.4, p. 483 [ doi:10.1107/97809553602060000857 ]
... of structure factors or, even better, diffraction images. References Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X- ...
Confidence in restraints versus information from diffraction
International Tables for Crystallography (2012). Vol. F, Section 18.3.3.1, p. 483 [ doi:10.1107/97809553602060000857 ]
Confidence in restraints versus information from diffraction 18.3.3.1. Confidence in restraints versus information from diffraction Primarily in cases of new structures, such as small-ligand- or metal-binding proteins, the refinement may indicate that the expected geometries and applied restraints seem incompatible with evidence from the electron density. Several sources for ...
[more results from section 18.3.3 in volume F]
Automated search procedures
International Tables for Crystallography (2012). Vol. F, Section 12.2.4.2, p. 330 [ doi:10.1107/97809553602060000838 ]
... be faster than traditional sequential searches. References Badger, J. & Athay, R. (1998). Automated and graphical methods for locating heavy-atom ...
[more results from section 12.2.4 in volume F]
The difference Fourier
International Tables for Crystallography (2012). Vol. F, Section 12.2.3, p. 329 [ doi:10.1107/97809553602060000838 ]
The difference Fourier 12.2.3. The difference Fourier Once the heavy-atom positions have been found, they can be used to calculate approximate phases and Fourier maps. Ideally, difference Fourier maps calculated with phases from a single site should reveal the other positions determined from the Harker search procedure. This ensures that ...
The Patterson function
International Tables for Crystallography (2012). Vol. F, Section 12.2.2, pp. 328-329 [ doi:10.1107/97809553602060000838 ]
... groups. Acta Cryst. 9, 867-873. Richardson, J. W. & Jacobson, R. A. (1987). In Patterson and Pattersons, edited by J. ...
The origin of the phase problem
International Tables for Crystallography (2012). Vol. F, Section 12.2.1, pp. 327-328 [ doi:10.1107/97809553602060000838 ]
... Steinbacher, S., Humm, A., Prade, L., Neuefeind, T., Moroder, L. & Huber, R. (1997). Bioincorporation of telluromethionine into proteins: a promising new ... haemoglobin IV. Sign determination by the isomorphous replacement method. Proc. R. Soc. London Ser. A, 225, 287-307. Hendrickson, W. ...
High levels of substitution; noncrystallographic symmetry
International Tables for Crystallography (2012). Vol. F, Section 12.2.5.3, p. 331 [ doi:10.1107/97809553602060000838 ]
... 346-361. Stubbs, M. T., Nar, H., Löwe, J. , Huber, R., Ladenstein, R., Spangfort, M. D. & Svensson, L. A. (1996). Locating ...
[more results from section 12.2.5 in volume F]
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3, pp. 477-481 [ doi:10.1107/97809553602060000857 ]
... amino-acid side chains EH denotes the values of Engh & Huber (1991), which were clustered according to atom type. The EH99 ... CH2 as CA, required new atom-type definitions for Engh & Huber (EH) (1991) parameterization to account for parameter-average differences of ... angles (°) of peptide backbone fragments EH denotes parameters from Engh & Huber (1991). Bold values mark important updates for angles ...
[more results from section 18.3.2 in volume F]
Risk of restraints: bias, lack of cross validation
International Tables for Crystallography (2012). Vol. F, Section 18.3.1.2, p. 474 [ doi:10.1107/97809553602060000857 ]
... preferentially chosen in model building, exaggerating their frequency. References Hooft, R. W. W., Sander, C. & Vriend, G. (1997). Objectively judging ...
[more results from section 18.3.1 in volume F]
Structure quality and target parameters
International Tables for Crystallography (2012). Vol. F, ch. 18.3, pp. 474-484 [ doi:10.1107/97809553602060000857 ]
... the CSD have come into widespread use for protein (Engh & Huber, 1991; Brünger, 1993; Priestle, 1994) and nucleic acid (Parkinson ... amino-acid side chains EH denotes the values of Engh & Huber (1991), which were clustered according to atom type. The EH99 ... CH2 as CA, required new atom-type definitions for Engh & Huber (EH) (1991) parameterization to account for parameter-average differences ...
Future perspectives
International Tables for Crystallography (2012). Vol. F, Section 18.3.4, p. 483 [ doi:10.1107/97809553602060000857 ]
... of structure factors or, even better, diffraction images. References Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X- ...
Confidence in restraints versus information from diffraction
International Tables for Crystallography (2012). Vol. F, Section 18.3.3.1, p. 483 [ doi:10.1107/97809553602060000857 ]
Confidence in restraints versus information from diffraction 18.3.3.1. Confidence in restraints versus information from diffraction Primarily in cases of new structures, such as small-ligand- or metal-binding proteins, the refinement may indicate that the expected geometries and applied restraints seem incompatible with evidence from the electron density. Several sources for ...
[more results from section 18.3.3 in volume F]
Automated search procedures
International Tables for Crystallography (2012). Vol. F, Section 12.2.4.2, p. 330 [ doi:10.1107/97809553602060000838 ]
... be faster than traditional sequential searches. References Badger, J. & Athay, R. (1998). Automated and graphical methods for locating heavy-atom ...
[more results from section 12.2.4 in volume F]
The difference Fourier
International Tables for Crystallography (2012). Vol. F, Section 12.2.3, p. 329 [ doi:10.1107/97809553602060000838 ]
The difference Fourier 12.2.3. The difference Fourier Once the heavy-atom positions have been found, they can be used to calculate approximate phases and Fourier maps. Ideally, difference Fourier maps calculated with phases from a single site should reveal the other positions determined from the Harker search procedure. This ensures that ...
The Patterson function
International Tables for Crystallography (2012). Vol. F, Section 12.2.2, pp. 328-329 [ doi:10.1107/97809553602060000838 ]
... groups. Acta Cryst. 9, 867-873. Richardson, J. W. & Jacobson, R. A. (1987). In Patterson and Pattersons, edited by J. ...
The origin of the phase problem
International Tables for Crystallography (2012). Vol. F, Section 12.2.1, pp. 327-328 [ doi:10.1107/97809553602060000838 ]
... Steinbacher, S., Humm, A., Prade, L., Neuefeind, T., Moroder, L. & Huber, R. (1997). Bioincorporation of telluromethionine into proteins: a promising new ... haemoglobin IV. Sign determination by the isomorphous replacement method. Proc. R. Soc. London Ser. A, 225, 287-307. Hendrickson, W. ...
High levels of substitution; noncrystallographic symmetry
International Tables for Crystallography (2012). Vol. F, Section 12.2.5.3, p. 331 [ doi:10.1107/97809553602060000838 ]
... 346-361. Stubbs, M. T., Nar, H., Löwe, J. , Huber, R., Ladenstein, R., Spangfort, M. D. & Svensson, L. A. (1996). Locating ...
[more results from section 12.2.5 in volume F]
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