[phenixbb] Very low resolution data set

Xiang Li li338 at purdue.edu
Wed Jul 3 13:42:15 PDT 2013

Hi everyone,

I am working on a very low resolution data set (14 A). It is a designed DNA crystal and unit cell size & symmetry fit well with the assumption. When I do the refinement I found the Rfree is extreme high, ~0.49 while Rwork is about 0.4. But the model seems fits in well with the density map. I have collected different datasets, and it gives about the same MR result for different sets.

I do not have any experience to work with low resolution data. Here I have a few questions:
1 What is the expected Rfree and Rwork for such low resolution data? I looked up PDB bank, and there is a 11.5A crystal with Rfree=~0.4. But not sure whether there is a kind of value for Rfree to consider the refinement works or not. 
2 There might be overfit problem during the refinement. Currently what I did  is to optimize the weight with PHENIX gui, add restraints between basepairs and NCS restraint. I tried to manually adjust the weight, but seems the optimized weight gives the best result. Are there other things I should try?
3 How to confirm that the result is real? There will be larger than usual error for such low resolution data, and what the supposed range should be?

Thanks a lot for your suggestions and help!


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