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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.

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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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SD of coordinates of rebuilt models (precision) estimated using ensembles with different starting models in a synthetic data set. The ordinates are the SD of coordinates in the single ensemble obtained by rebuilding at a resolution of 1.75 Å listed in Table 3 ▶. The abscissas are the SD of the coordinates of the corresponding atoms in the six ensembles (1–6) in Table 4 ▶, rebuilt at the same resolution but using different starting models. (a) Main-chain atoms. (b) Side-chain atoms.
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fig7: SD of coordinates of rebuilt models (precision) estimated using ensembles with different starting models in a synthetic data set. The ordinates are the SD of coordinates in the single ensemble obtained by rebuilding at a resolution of 1.75 Å listed in Table 3 ▶. The abscissas are the SD of the coordinates of the corresponding atoms in the six ensembles (1–6) in Table 4 ▶, rebuilt at the same resolution but using different starting models. (a) Main-chain atoms. (b) Side-chain atoms.

Mentions: The reproducibility of the estimates of precision obtained from ensembles of models rebuilt at a resolution of 1.75 Å was also examined. Fig. 7 ▶ compares the precision of the models, atom by atom, estimated from ensembles 1–6 in Table 4 ▶, with the precision estimated from the single ensemble generated in the separate analysis at a resolution of 1.75 Å in Table 3 ▶. Fig. 7 ▶(a) compares the SD of coordinates for main-chain atoms and Fig. 7 ▶(b) for side-chain atoms. While the SDs of the coordinates in the two cases are not identical, they are similar, with an overall correlation coefficient of 0.73 for main-chain atoms and 0.65 for side-chain atoms.


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)

SD of coordinates of rebuilt models (precision) estimated using ensembles with different starting models in a synthetic data set. The ordinates are the SD of coordinates in the single ensemble obtained by rebuilding at a resolution of 1.75 Å listed in Table 3 ▶. The abscissas are the SD of the coordinates of the corresponding atoms in the six ensembles (1–6) in Table 4 ▶, rebuilt at the same resolution but using different starting models. (a) Main-chain atoms. (b) Side-chain atoms.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig7: SD of coordinates of rebuilt models (precision) estimated using ensembles with different starting models in a synthetic data set. The ordinates are the SD of coordinates in the single ensemble obtained by rebuilding at a resolution of 1.75 Å listed in Table 3 ▶. The abscissas are the SD of the coordinates of the corresponding atoms in the six ensembles (1–6) in Table 4 ▶, rebuilt at the same resolution but using different starting models. (a) Main-chain atoms. (b) Side-chain atoms.
Mentions: The reproducibility of the estimates of precision obtained from ensembles of models rebuilt at a resolution of 1.75 Å was also examined. Fig. 7 ▶ compares the precision of the models, atom by atom, estimated from ensembles 1–6 in Table 4 ▶, with the precision estimated from the single ensemble generated in the separate analysis at a resolution of 1.75 Å in Table 3 ▶. Fig. 7 ▶(a) compares the SD of coordinates for main-chain atoms and Fig. 7 ▶(b) for side-chain atoms. While the SDs of the coordinates in the two cases are not identical, they are similar, with an overall correlation coefficient of 0.73 for main-chain atoms and 0.65 for side-chain atoms.

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