Ganesh Jawahar Swaminathan wrote:
> I am trying to solve the structure of a protein with MR using a
> model that has low homology to the protein I am trying to solve
> (45%). Rotation and Translation Function Results are quite encouraging
> but refinement in X-PLOR show the crystallographic R to continually
> decrease while the Free R stays at a high level. I end up with
> situations of 17%R and 46%Free R.
> I guess this problems may be due to low sequene homology. But what is
> the real significance of this value other than overfitting the data
> to the model ? Also what are the ways out of this problems.
The case of 46% R-free/ 17% R is an extreme example of overfitting the data.
The weigths in refinement are such that refinement is almost meaningless.
What may help:
1.) Increasing number of observables
increasing the resolution of data (both towards low and high res),
inclusion of weak reflections
2.) Increasing weigth of stereochemistry
3.) Deletion of doubtful segments, e.g non-homologous loops
4.) Initial segmental rigid body refinement
All of the above is likely to increase regular R-factor.
Higher R-factor is of no significance.
5.) Check for alternative solution related by translation to your current
solution.
45 a.a. identity is not low for molecular replecement.
--
Zbyszek Otwinowski | zbyszek at chop.swmed.edu
University of Texas | tel : (214)-648-5098
Southwestern Medical Center | fax : (214)-648-5095
5323 Harry Hines Boulevard Dallas, Texas 75235-9038
[EOB]
