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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) compared with SD of coordinates of perfect models used to create synthetic crystal. (a) Main-chain atoms of models rebuilt at a resolution of 1.75 Å. (b) Side-chain atoms of models rebuilt at a resolution of 1.75 Å. (c) Main-chain atoms of models rebuilt at a resolution of 4.0 Å. (d) Side-chain atoms of models rebuilt at a resolution of 4.0 Å.
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fig5: SD of coordinates of rebuilt models (precision) compared with SD of coordinates of perfect models used to create synthetic crystal. (a) Main-chain atoms of models rebuilt at a resolution of 1.75 Å. (b) Side-chain atoms of models rebuilt at a resolution of 1.75 Å. (c) Main-chain atoms of models rebuilt at a resolution of 4.0 Å. (d) Side-chain atoms of models rebuilt at a resolution of 4.0 Å.

Mentions: Despite this conclusion, we expect that the heterogeneity in a crystal does contribute to diversity among multiple rebuilt models, perhaps even on an atom-by-atom or residue-by-residue basis. For example, it seems likely that those parts of a structure that have a high degree of heterogeneity will typically be rebuilt with less reproducibility than those that are more uniform. The analysis in Table 3 ▶ simply shows that the variability among rebuilt models is dominated by the effects of the amount of data available and that the variability among rebuilt models is not necessarily even on the same scale as the heterogeneity among structures in the crystal. Fig. 5 ▶ illustrates this relationship. In Fig. 5 ▶(a), the SD of main-chain coordinates among models rebuilt at a resolution of 1.75 Å is plotted as a function of the SD of coordinates in the ‘perfect’ models used to construct the synthetic ‘crystal’. There is some correlation of the heterogeneity in the two cases, but the scale of variation in the rebuilt models is much smaller than that of the original perfect models. Fig. 5 ▶(b) shows a similar result for side-chain atoms. Figs. 5 ▶(c) and 5 ▶(d) show the same relation as Figs. 5 ▶(a) and 5 ▶(b), except that the models rebuilt at a resolution of 4 Å are considered. In this case, the scale of variation in the rebuilt models is similar to that of the original perfect models. A consideration of Figs. 5 ▶(c) and 5 ▶(d) alone might lead to the conclusion that there is a general relationship between ensembles of rebuilt models and the contents of the crystal. However, considering that Figs. 5 ▶(c) and 5 ▶(d) differ from Figs. 5 ▶(a) and 5 ▶(b) only in the truncation of the data to a resolution of 4 Å, it is clear that there is no such general relationship. A more likely interpretation of Figs. 5 ▶(c) and 5 ▶(d) is that the heterogeneity in the ‘crystal’ in some locations leads to a map with relatively poor definition in those locations and thereby to a set of rebuilt models with higher heterogeneity in those locations. The extent of heterogeneity of the rebuilt models, however, depends strongly on the resolution of the data used to create the map, so that the heterogeneity in the rebuilt models is not a quantitative indicator of the heterogeneity in the crystal.


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) compared with SD of coordinates of perfect models used to create synthetic crystal. (a) Main-chain atoms of models rebuilt at a resolution of 1.75 Å. (b) Side-chain atoms of models rebuilt at a resolution of 1.75 Å. (c) Main-chain atoms of models rebuilt at a resolution of 4.0 Å. (d) Side-chain atoms of models rebuilt at a resolution of 4.0 Å.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig5: SD of coordinates of rebuilt models (precision) compared with SD of coordinates of perfect models used to create synthetic crystal. (a) Main-chain atoms of models rebuilt at a resolution of 1.75 Å. (b) Side-chain atoms of models rebuilt at a resolution of 1.75 Å. (c) Main-chain atoms of models rebuilt at a resolution of 4.0 Å. (d) Side-chain atoms of models rebuilt at a resolution of 4.0 Å.
Mentions: Despite this conclusion, we expect that the heterogeneity in a crystal does contribute to diversity among multiple rebuilt models, perhaps even on an atom-by-atom or residue-by-residue basis. For example, it seems likely that those parts of a structure that have a high degree of heterogeneity will typically be rebuilt with less reproducibility than those that are more uniform. The analysis in Table 3 ▶ simply shows that the variability among rebuilt models is dominated by the effects of the amount of data available and that the variability among rebuilt models is not necessarily even on the same scale as the heterogeneity among structures in the crystal. Fig. 5 ▶ illustrates this relationship. In Fig. 5 ▶(a), the SD of main-chain coordinates among models rebuilt at a resolution of 1.75 Å is plotted as a function of the SD of coordinates in the ‘perfect’ models used to construct the synthetic ‘crystal’. There is some correlation of the heterogeneity in the two cases, but the scale of variation in the rebuilt models is much smaller than that of the original perfect models. Fig. 5 ▶(b) shows a similar result for side-chain atoms. Figs. 5 ▶(c) and 5 ▶(d) show the same relation as Figs. 5 ▶(a) and 5 ▶(b), except that the models rebuilt at a resolution of 4 Å are considered. In this case, the scale of variation in the rebuilt models is similar to that of the original perfect models. A consideration of Figs. 5 ▶(c) and 5 ▶(d) alone might lead to the conclusion that there is a general relationship between ensembles of rebuilt models and the contents of the crystal. However, considering that Figs. 5 ▶(c) and 5 ▶(d) differ from Figs. 5 ▶(a) and 5 ▶(b) only in the truncation of the data to a resolution of 4 Å, it is clear that there is no such general relationship. A more likely interpretation of Figs. 5 ▶(c) and 5 ▶(d) is that the heterogeneity in the ‘crystal’ in some locations leads to a map with relatively poor definition in those locations and thereby to a set of rebuilt models with higher heterogeneity in those locations. The extent of heterogeneity of the rebuilt models, however, depends strongly on the resolution of the data used to create the map, so that the heterogeneity in the rebuilt models is not a quantitative indicator of the heterogeneity in the crystal.

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