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The befores and afters of molecular replacement.

Dodson E - Acta Crystallogr. D Biol. Crystallogr. (2007)

Bottom Line: Sequence matching can suggest whether there is a suitable three-dimensional model available, but it is also important to analyse the model in order to find its likely oligomeric state and to establish whether there are likely to be domain movements.Once a solution has been found it must be refined, which can be challenging for low-homology models.There is a detailed discussion of structures used as examples for CCP4 tutorials.

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Affiliation: York Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5DD, England. e.dodson@ysbl.york.ac.uk

ABSTRACT
This review addresses the essential questions to consider when attempting to phase a new crystal structure using molecular replacement. Sequence matching can suggest whether there is a suitable three-dimensional model available, but it is also important to analyse the model in order to find its likely oligomeric state and to establish whether there are likely to be domain movements. Once a solution has been found it must be refined, which can be challenging for low-homology models. There is a detailed discussion of structures used as examples for CCP4 tutorials.

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The first maximum-likelihood weighted electron-density map for S100 from the 1irj solution after ten initial rounds of refinement. The model had been truncated to remove many of the side chains. R and R                  free had fallen from 47.1% and 47.2% to 34.4% and 44.4%, respectively. Although the map is of poor quality, there is clear density for the Ile79 side chain.
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fig6: The first maximum-likelihood weighted electron-density map for S100 from the 1irj solution after ten initial rounds of refinement. The model had been truncated to remove many of the side chains. R and R free had fallen from 47.1% and 47.2% to 34.4% and 44.4%, respectively. Although the map is of poor quality, there is clear density for the Ile79 side chain.

Mentions: The usual check is that the solution model generates structure amplitudes which agree with the observed ones. Initial R values always seem to be high (typically R/free R of 55%/55% for me), but correct solutions will (usually!) refine automatically to an R/free R of about 40%/45%. The most encouraging verification is the electron density: if you can see features in the maps which are not part of the model, then the solution is probably substantially correct (Fig. 6 ▶).


The befores and afters of molecular replacement.

Dodson E - Acta Crystallogr. D Biol. Crystallogr. (2007)

The first maximum-likelihood weighted electron-density map for S100 from the 1irj solution after ten initial rounds of refinement. The model had been truncated to remove many of the side chains. R and R                  free had fallen from 47.1% and 47.2% to 34.4% and 44.4%, respectively. Although the map is of poor quality, there is clear density for the Ile79 side chain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394785&req=5

fig6: The first maximum-likelihood weighted electron-density map for S100 from the 1irj solution after ten initial rounds of refinement. The model had been truncated to remove many of the side chains. R and R free had fallen from 47.1% and 47.2% to 34.4% and 44.4%, respectively. Although the map is of poor quality, there is clear density for the Ile79 side chain.
Mentions: The usual check is that the solution model generates structure amplitudes which agree with the observed ones. Initial R values always seem to be high (typically R/free R of 55%/55% for me), but correct solutions will (usually!) refine automatically to an R/free R of about 40%/45%. The most encouraging verification is the electron density: if you can see features in the maps which are not part of the model, then the solution is probably substantially correct (Fig. 6 ▶).

Bottom Line: Sequence matching can suggest whether there is a suitable three-dimensional model available, but it is also important to analyse the model in order to find its likely oligomeric state and to establish whether there are likely to be domain movements.Once a solution has been found it must be refined, which can be challenging for low-homology models.There is a detailed discussion of structures used as examples for CCP4 tutorials.

View Article: PubMed Central - HTML - PubMed

Affiliation: York Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5DD, England. e.dodson@ysbl.york.ac.uk

ABSTRACT
This review addresses the essential questions to consider when attempting to phase a new crystal structure using molecular replacement. Sequence matching can suggest whether there is a suitable three-dimensional model available, but it is also important to analyse the model in order to find its likely oligomeric state and to establish whether there are likely to be domain movements. Once a solution has been found it must be refined, which can be challenging for low-homology models. There is a detailed discussion of structures used as examples for CCP4 tutorials.

Show MeSH