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Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, Adams PD - Acta Crystallogr. D Biol. Crystallogr. (2007)

Bottom Line: Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization.The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29.The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.

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Affiliation: Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

ABSTRACT
The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.

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Completeness of main-chain model (closed diamonds) and assignment of residues to sequence (open triangles) of final models in Fig. 2 ▶. (a) Completeness as a function of resolution of the data used in modelling. (b) Completeness as a function of the correlation coefficient of the starting density-modified experimental map to the model map. (c) Completeness as a function of resolution as in (a), except that only structures with a correlation coefficient of the starting density-modified experimental map of greater than 0.85 are included.
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fig3: Completeness of main-chain model (closed diamonds) and assignment of residues to sequence (open triangles) of final models in Fig. 2 ▶. (a) Completeness as a function of resolution of the data used in modelling. (b) Completeness as a function of the correlation coefficient of the starting density-modified experimental map to the model map. (c) Completeness as a function of resolution as in (a), except that only structures with a correlation coefficient of the starting density-modified experimental map of greater than 0.85 are included.

Mentions: Figs. 3 ▶(a) and 3 ▶(b) illustrate the completeness of the models obtained as a function of the resolution of the data and of the quality of the starting density-modified electron-density map. The median percentage of residues built is 95% and the median percentage of residues assigned to the sequence is 90% (means of 90% and 78%, respectively). The percentage of residues built depends more on the quality of the starting map than on the resolution of the data, although neither of these variables correlates very closely with the completeness of the models. Fig. 3 ▶(c) illustrates that the completeness of the models is somewhat related to the resolution of the data for the subset of cases where a high-quality (map CC > 0.85) starting density-modified map was available, but only weakly so.


Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, Adams PD - Acta Crystallogr. D Biol. Crystallogr. (2007)

Completeness of main-chain model (closed diamonds) and assignment of residues to sequence (open triangles) of final models in Fig. 2 ▶. (a) Completeness as a function of resolution of the data used in modelling. (b) Completeness as a function of the correlation coefficient of the starting density-modified experimental map to the model map. (c) Completeness as a function of resolution as in (a), except that only structures with a correlation coefficient of the starting density-modified experimental map of greater than 0.85 are included.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394820&req=5

fig3: Completeness of main-chain model (closed diamonds) and assignment of residues to sequence (open triangles) of final models in Fig. 2 ▶. (a) Completeness as a function of resolution of the data used in modelling. (b) Completeness as a function of the correlation coefficient of the starting density-modified experimental map to the model map. (c) Completeness as a function of resolution as in (a), except that only structures with a correlation coefficient of the starting density-modified experimental map of greater than 0.85 are included.
Mentions: Figs. 3 ▶(a) and 3 ▶(b) illustrate the completeness of the models obtained as a function of the resolution of the data and of the quality of the starting density-modified electron-density map. The median percentage of residues built is 95% and the median percentage of residues assigned to the sequence is 90% (means of 90% and 78%, respectively). The percentage of residues built depends more on the quality of the starting map than on the resolution of the data, although neither of these variables correlates very closely with the completeness of the models. Fig. 3 ▶(c) illustrates that the completeness of the models is somewhat related to the resolution of the data for the subset of cases where a high-quality (map CC > 0.85) starting density-modified map was available, but only weakly so.

Bottom Line: Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization.The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29.The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

ABSTRACT
The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.

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