Dear Sampath, You are right, the gap between R and Rfree is significant and indicates that your model was overfitted. Without knowing your data or your model, some reasons for overfitting might be: - you used automated placement of water molecules (e.g. through arpwaters or in coot) and never checked the water molecules for chemical reasonability. How many residues are there in your structure and how many water molecules? - there might be a domain that - despite the resolution - does not resolve with your data but you built somethig nevertheless - you build things into your model while using a too low (approx. <1.0sigma) sigma-level for your map. At too low a contour level you can often see what you _want_ to see in my experience, and not what is there - you screwed up the Rfree set and it's not indendent anymore. However, in that case I would rather expect the difference or the ration to be too small rather than too big. - Your data may be twinned.
That's just a first set of reasons but there might be something one could only know by looking at your data. Tim On Wed, Jul 07, 2010 at 10:17:14PM -0700, Sampath Natarajan wrote: > Dear all, > > I have a question about the R free value. I refined a structure with 2A > resolution. After model building and restraint refinement using Refmac > program, the average B factor was around 50 for all atoms. The R/Rfree were > around 22/34. Then used the TLS refinement choosing entire molecule. Then > R/Rfree reduced as 20/32. But the average B factor was reduced as 30. The > R/Rfree difference is about 12% in final refinement. I feel it is > significantly higher. > > Could any one suggest me to reduce the Rfree value more? or is it good to > submit the data in the PDB database with this 12% difference? > > Thanks for the suggestions. > > Sincerely, > Sampath N -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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