Numerology<i>versus</i>reality: a voice in a recent dispute

Jaskólski, Mariusz; Gilski, Mirosław; Dauter, Zbigniew; Wlodawer, Alexander

doi:10.1107/s0907444907049359

Cited by 34 publications

(52 citation statements)

References 7 publications

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“…By examining the HEWL test case we traced the source of this behavior to the stretches of polypeptide where the main chain adopts two conformations. [This problem had been noted by Jaskolski et al (2007) in their analysis of the HEWL model.] The fit of these regions to either library is far worse than the fit of the full occupancy regions.…”

Section: Test Cases and Assessment Strategymentioning

confidence: 96%

A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

Tronrud

Karplus

2011

Acta Crystallogr D Biol Cryst

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To utilize a new conformation-dependent backbone-geometry library (CDL) in protein refinements at atomic resolution, a script was written that creates a restraint file for the SHELXL refinement program. It was found that the use of this library allows models to be created that have a substantially better fit to main-chain bond angles and lengths without degrading their fit to the X-ray data even at resolutions near 1 Å . For models at much higher resolution ($0.7 Å ), the refined model for parts adopting single well occupied positions is largely independent of the restraints used, but these structures still showed much smaller r.m.s.d. residuals when assessed with the CDL. Examination of the refinement tests across a wide resolution range from 2.4 to 0.65 Å revealed consistent behavior supporting the use of the CDL as a next-generation restraint library to improve refinement. CDL restraints can be generated using the service at

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Section: Test Cases and Assessment Strategymentioning

confidence: 96%

A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

Tronrud

Karplus

2011

Acta Crystallogr D Biol Cryst

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“…We preferred to avoid scales that were fixed at standards for geometric characteristics (see, for example, Jaskolski et al, 2007;Stec, 2007) or R factors (Tickle et al, 1998(Tickle et al, , 2000. Instead, we referred to previously solved models.…”

Section: Scaling and Colouringmentioning

confidence: 99%

“…When choosing the models for comparison, one may exclude ambiguous models, for example those with a negative difference R free À R or those that are formally correct but disagree with advanced analysis (see, for example, Jaskolski et al, 2007). The further choice of control models depends on the questions that are posed.…”

Section: Models For Comparisonmentioning

confidence: 99%

Crystallographic model quality at a glance

Urzhumtseva

Afonine

Adams

et al. 2009

Acta Crystallogr D Biol Crystallogr

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A crystallographic macromolecular model is typically characterized by a list of quality criteria, such as R factors, deviations from ideal stereochemistry and average B factors, which are usually provided as tables in publications or in structural databases. In order to facilitate a quick model-quality evaluation, a graphical representation is proposed. Each key parameter such as R factor or bond-length deviation from 'ideal values' is shown graphically as a point on a 'ruler'. These rulers are plotted as a set of lines with the same origin, forming a hub and spokes. Different parts of the rulers are coloured differently to reflect the frequency (red for a low frequency, blue for a high frequency) with which the corresponding values are observed in a reference set of structures determined previously. The points for a given model marked on these lines are connected to form a polygon. A polygon that is strongly compressed or dilated along some axes reveals unusually low or high values of the corresponding characteristics. Polygon vertices in 'red zones' indicate parameters which lie outside typical values.

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“…Validation of the models with MolProbity (Chen et al, 2010) revealed a small number of disagreements with the 'standard' macromolecular geometric target values. However, the values stored in the restraint target libraries are affected by uncertainties significantly larger than the level of accuracy obtained here (Jaskolski et al, 2007) and consequently cannot be treated as absolutely faithful targets.…”

Section: Geometric Parametersmentioning

confidence: 99%

Transferable aspherical atom model refinement of protein and DNA structures against ultra-high-resolution X-ray data

Malińska¹,

Dauter²

2015

Acta Cryst Sect A

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In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.

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Numerologyversusreality: a voice in a recent dispute

Cited by 34 publications

References 7 publications

A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

Crystallographic model quality at a glance

Transferable aspherical atom model refinement of protein and DNA structures against ultra-high-resolution X-ray data

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