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Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models.

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

Bottom Line: Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface.Synthetic data were created in which a crystal structure was modelled as the average of a set of ;perfect' structures and the range of models obtained by rebuilding a single starting model was examined.Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models.

View Article: PubMed Central - HTML - PubMed

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

ABSTRACT
Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be created. Sets of models were generated in this way using real data for ten protein structures from the Protein Data Bank and using synthetic data generated at various resolutions. Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface. Possible interpretations of the variation among models created by repetitive rebuilding were investigated. Synthetic data were created in which a crystal structure was modelled as the average of a set of ;perfect' structures and the range of models obtained by rebuilding a single starting model was examined. The standard deviations of coordinates in models obtained by repetitive rebuilding at high resolution are small, while those obtained for the same synthetic crystal structure at low resolution are large, so that the diversity within a group of models cannot generally be a quantitative reflection of the actual structures in a crystal. Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models.

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Models used to create synthetic ‘crystal’. (a) PyMOL view (DeLano, 2002 ▶) of 20 ‘perfect’ models in the ensemble used to create a synthetic data set. (b) Perfect models and perfect electron density corresponding to those models.
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fig4: Models used to create synthetic ‘crystal’. (a) PyMOL view (DeLano, 2002 ▶) of 20 ‘perfect’ models in the ensemble used to create a synthetic data set. (b) Perfect models and perfect electron density corresponding to those models.

Mentions: As mentioned above, the interpretation of ensembles of models created by repetitive model building, density modification and refinement procedures such as those used here is currently an open question (Furnham et al., 2006 ▶; de Bakker et al., 2006 ▶). In particular, it is not known whether the heterogeneity among these models reflects the contents of the crystal itself or whether it instead reflects the precision to which a particular model can be specified or some combination of these. To address this question, synthetic data were created based on the structure of initiation factor 5A from P. aerophilum in which the contents of the ‘crystal’ are known exactly. The contents of a crystal were modelled as a collection of 20 structures with an r.m.s.d. of 1.5 Å from the refined IF5A structure, model structure factors were calculated based on these structures (including a bulk-solvent model), 10% random error was added and the resulting structure factors were used as ‘experimental’ data. Fig. 4 ▶ illustrates a portion of this ensemble of ‘perfect’ structures and the model electron-density map calculated from their average. The models are quite heterogeneous, but the resulting electron-density map looks much like a real electron-density map that might be obtained at a resolution of about 2–2.5 Å.


Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models.

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

Models used to create synthetic ‘crystal’. (a) PyMOL view (DeLano, 2002 ▶) of 20 ‘perfect’ models in the ensemble used to create a synthetic data set. (b) Perfect models and perfect electron density corresponding to those models.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483474&req=5

fig4: Models used to create synthetic ‘crystal’. (a) PyMOL view (DeLano, 2002 ▶) of 20 ‘perfect’ models in the ensemble used to create a synthetic data set. (b) Perfect models and perfect electron density corresponding to those models.
Mentions: As mentioned above, the interpretation of ensembles of models created by repetitive model building, density modification and refinement procedures such as those used here is currently an open question (Furnham et al., 2006 ▶; de Bakker et al., 2006 ▶). In particular, it is not known whether the heterogeneity among these models reflects the contents of the crystal itself or whether it instead reflects the precision to which a particular model can be specified or some combination of these. To address this question, synthetic data were created based on the structure of initiation factor 5A from P. aerophilum in which the contents of the ‘crystal’ are known exactly. The contents of a crystal were modelled as a collection of 20 structures with an r.m.s.d. of 1.5 Å from the refined IF5A structure, model structure factors were calculated based on these structures (including a bulk-solvent model), 10% random error was added and the resulting structure factors were used as ‘experimental’ data. Fig. 4 ▶ illustrates a portion of this ensemble of ‘perfect’ structures and the model electron-density map calculated from their average. The models are quite heterogeneous, but the resulting electron-density map looks much like a real electron-density map that might be obtained at a resolution of about 2–2.5 Å.

Bottom Line: Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface.Synthetic data were created in which a crystal structure was modelled as the average of a set of ;perfect' structures and the range of models obtained by rebuilding a single starting model was examined.Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models.

View Article: PubMed Central - HTML - PubMed

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

ABSTRACT
Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be created. Sets of models were generated in this way using real data for ten protein structures from the Protein Data Bank and using synthetic data generated at various resolutions. Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface. Possible interpretations of the variation among models created by repetitive rebuilding were investigated. Synthetic data were created in which a crystal structure was modelled as the average of a set of ;perfect' structures and the range of models obtained by rebuilding a single starting model was examined. The standard deviations of coordinates in models obtained by repetitive rebuilding at high resolution are small, while those obtained for the same synthetic crystal structure at low resolution are large, so that the diversity within a group of models cannot generally be a quantitative reflection of the actual structures in a crystal. Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models.

Show MeSH
Related in: MedlinePlus