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Results for DC.creator="R." AND DC.creator="Huber" in section 18.3.2 of volume F page 1 of 2 pages. |
Formulation of refinement restraints
International Tables for Crystallography (2012). Vol. F, Section 18.3.2, pp. 475-483 [ 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 ...
Special geometries: cofactors, ligands, metals etc.
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.8, pp. 482-483 [ doi:10.1107/97809553602060000857 ]
Special geometries: cofactors, ligands, metals etc. 18.3.2.8. Special geometries: cofactors, ligands, metals etc. Most crystallographers will experience neither the need nor desire to derive their own parameterization for general protein structure refinement; many, however, need new parameters for ligands or other entities that are not amino-acid residues. The accuracy required ...
Effects of hydrogen atoms in parameterization
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.7, p. 482 [ doi:10.1107/97809553602060000857 ]
Effects of hydrogen atoms in parameterization 18.3.2.7. Effects of hydrogen atoms in parameterization While many CSD fragments include hydrogen-atom positions, their accuracy is necessarily the most limited. Evaluation of CSD statistics without hydrogens and the subsequent addition of parameters to refine hydrogens adds an additional artifactual coupling between parameters involving ...
Non-bonded interactions
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.6, p. 482 [ doi:10.1107/97809553602060000857 ]
Non-bonded interactions 18.3.2.6. Non-bonded interactions Like the potential parameterization of torsion-angle statistics with the CSD, parameterization of non-bonded interactions, typically into terms representing packing (an empirical mix of London dispersion forces and solvent effects), electrostatics and hydrogen bonding, is probably more strongly influenced by protein environment than ...
Torsion angles
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.5, p. 482 [ doi:10.1107/97809553602060000857 ]
Torsion angles 18.3.2.5. Torsion angles Since torsion angles are generally more adequately determined by protein structures of typical resolutions, there is less need to derive parameters from the CSD for refinement purposes. Further, distributions derived from small molecules may not be representative of torsion angles among proteins, since typical fragments lack ...
Planarity restraints
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.4, pp. 481-482 [ doi:10.1107/97809553602060000857 ]
... molecules. References Marquart, M., Walter, J., Deisenhofer, J., Bode, W. & Huber, R. (1983). The geometry of the reactive site and of ...
Sulfur-containing residues: methionine, cysteine, disulfides
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.7, p. 481 [ doi:10.1107/97809553602060000857 ]
Sulfur-containing residues: methionine, cysteine, disulfides 18.3.2.3.7. Sulfur-containing residues: methionine, cysteine, disulfides One of the most conspicuous features of the EH parameters is the soft force constant for the methionine SD-CE bond length. The 49 fragments now in the CSD also show a sample deviation for the 1.774Å average ...
Basic residues: arginine, lysine
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.6, p. 481 [ doi:10.1107/97809553602060000857 ]
Basic residues: arginine, lysine 18.3.2.3.6. Basic residues: arginine, lysine The 98 arginine fragments in the database did not show alterations from the EH values, except generally tighter restraints at the guanidinium group. Lysine CD-CE bond lengths are somewhat shorter in the new statistics, while the two angles derived from the ...
Acidic residues: glutamate, aspartate
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.5, p. 481 [ doi:10.1107/97809553602060000857 ]
Acidic residues: glutamate, aspartate 18.3.2.3.5. Acidic residues: glutamate, aspartate The fragment definitions were chosen to select both symmetrically and asymmetrically encoded carboxylate structures; that is, the statistics include carboxylate groups with delocalized charges as well as carboxylate groups encoded with a single charged oxygen atom. This distribution presumably reflects the variations ...
Neutral polar residues: serine, threonine, glutamine, asparagine
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.4, p. 481 [ doi:10.1107/97809553602060000857 ]
Neutral polar residues: serine, threonine, glutamine, asparagine 18.3.2.3.4. Neutral polar residues: serine, threonine, glutamine, asparagine These residues share neutral polarity, but are all geometrically distinct. Like leucine, valine and isoleucine described above, threonine is branched at CB, and the parameterization for C-CA-CB should be chosen accordingly. Additionally for threonine ...
International Tables for Crystallography (2012). Vol. F, Section 18.3.2, pp. 475-483 [ 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 ...
Special geometries: cofactors, ligands, metals etc.
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.8, pp. 482-483 [ doi:10.1107/97809553602060000857 ]
Special geometries: cofactors, ligands, metals etc. 18.3.2.8. Special geometries: cofactors, ligands, metals etc. Most crystallographers will experience neither the need nor desire to derive their own parameterization for general protein structure refinement; many, however, need new parameters for ligands or other entities that are not amino-acid residues. The accuracy required ...
Effects of hydrogen atoms in parameterization
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.7, p. 482 [ doi:10.1107/97809553602060000857 ]
Effects of hydrogen atoms in parameterization 18.3.2.7. Effects of hydrogen atoms in parameterization While many CSD fragments include hydrogen-atom positions, their accuracy is necessarily the most limited. Evaluation of CSD statistics without hydrogens and the subsequent addition of parameters to refine hydrogens adds an additional artifactual coupling between parameters involving ...
Non-bonded interactions
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.6, p. 482 [ doi:10.1107/97809553602060000857 ]
Non-bonded interactions 18.3.2.6. Non-bonded interactions Like the potential parameterization of torsion-angle statistics with the CSD, parameterization of non-bonded interactions, typically into terms representing packing (an empirical mix of London dispersion forces and solvent effects), electrostatics and hydrogen bonding, is probably more strongly influenced by protein environment than ...
Torsion angles
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.5, p. 482 [ doi:10.1107/97809553602060000857 ]
Torsion angles 18.3.2.5. Torsion angles Since torsion angles are generally more adequately determined by protein structures of typical resolutions, there is less need to derive parameters from the CSD for refinement purposes. Further, distributions derived from small molecules may not be representative of torsion angles among proteins, since typical fragments lack ...
Planarity restraints
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.4, pp. 481-482 [ doi:10.1107/97809553602060000857 ]
... molecules. References Marquart, M., Walter, J., Deisenhofer, J., Bode, W. & Huber, R. (1983). The geometry of the reactive site and of ...
Sulfur-containing residues: methionine, cysteine, disulfides
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.7, p. 481 [ doi:10.1107/97809553602060000857 ]
Sulfur-containing residues: methionine, cysteine, disulfides 18.3.2.3.7. Sulfur-containing residues: methionine, cysteine, disulfides One of the most conspicuous features of the EH parameters is the soft force constant for the methionine SD-CE bond length. The 49 fragments now in the CSD also show a sample deviation for the 1.774Å average ...
Basic residues: arginine, lysine
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.6, p. 481 [ doi:10.1107/97809553602060000857 ]
Basic residues: arginine, lysine 18.3.2.3.6. Basic residues: arginine, lysine The 98 arginine fragments in the database did not show alterations from the EH values, except generally tighter restraints at the guanidinium group. Lysine CD-CE bond lengths are somewhat shorter in the new statistics, while the two angles derived from the ...
Acidic residues: glutamate, aspartate
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.5, p. 481 [ doi:10.1107/97809553602060000857 ]
Acidic residues: glutamate, aspartate 18.3.2.3.5. Acidic residues: glutamate, aspartate The fragment definitions were chosen to select both symmetrically and asymmetrically encoded carboxylate structures; that is, the statistics include carboxylate groups with delocalized charges as well as carboxylate groups encoded with a single charged oxygen atom. This distribution presumably reflects the variations ...
Neutral polar residues: serine, threonine, glutamine, asparagine
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.4, p. 481 [ doi:10.1107/97809553602060000857 ]
Neutral polar residues: serine, threonine, glutamine, asparagine 18.3.2.3.4. Neutral polar residues: serine, threonine, glutamine, asparagine These residues share neutral polarity, but are all geometrically distinct. Like leucine, valine and isoleucine described above, threonine is branched at CB, and the parameterization for C-CA-CB should be chosen accordingly. Additionally for threonine ...
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