HI Sue,
Can you give rmsZ for the bond and angles (from the Refmac output)? I never could figure these rmsd values out...
I'm guessing that the restraint are too loose, or at least not optimal. Perhaps, they went overboard with the TLS as well (sometimes fewer TLS goups give much better R and R-free values). I'm not sure anything in particular is wrong with the data processing. They should optimize the restraint weights in refinement first. In this case tighter B-factor restraint weights might do the trick.
Gratuitous plug: throw the model and data into PDB_REDO (which uses Refmac too) and see if it gives better refinement results.
Cheers,
Robbie
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Roberts, Sue A - (suer)
> Sent: Wednesday, June 26, 2013 17:45
> To: [log in to unmask]
> Subject: [ccp4bb] R too low?
>
> Hello Everyone
>
> I have two data sets, from the same crystal form (space group P32) of the
> same protein, collected at 100 K at SSRL, about 2.2 A resolution, that refining
> to R = 0.14, Rf = 0.26 (refmac/TLS). This is a molecular replacement solution,
> from a model with about 40% homology (after MR density was apparent for
> some missing or misbuilt residues, so I don't think the structure is stuck in the
> wrong place. The Fo-Fc map is essentially featureless. The 2Fo-Fc map
> doesn't look as good as it should - for instance, there are very few water
> molecules to be found. The data reduction statistics look OK, the resolution
> cutoff is pretty conservative. There is one molecule in the asymmetric unit,
> so no NCS. There is no twinning either.
>
> It seemed to me that the R is too low, not Rf too high. More normally, R ends
> up about .18 - .20 for a data set at this resolution.
>
> I reprocessed the images with a different data processing program and redid
> the MR. The data reduction statistics look similar, the resolution is the same,
> but now the structure refines to R = 0.20, Rf = 0.24 (same free R set of
> reflections chosen, still refmac/TLS.) The maps look more normal. Further
> rebuilding took us to R = 0.18, Rf = 0.22
>
> So, the question I have (and that I've been asked by the student and PI) is:
> What was the problem with the original data set? What should I be looking
> for in the data reduction log files, for instance, or in the refinement log? The
> large R - free R spread is characteristic of overfitting, but the geometry is not
> too loose (rmsd bonds = 0.14), there are plenty of reflections (both working
> and free).
>
> Can anyone point me toward a reason R would be low?
>
> Thanks
>
> Sue
>
>
> Dr. Sue A. Roberts
> Dept. of Chemistry and Biochemistry
> University of Arizona
> 1041 E. Lowell St., Tucson, AZ 85721
> Phone: 520 621 8171 or 520 621 4168
> [log in to unmask]
> http://www.cbc.arizona.edu/xray or
> http://www.cbc.arizona.edu/facilities/x-ray_diffraction
>
>
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