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 [email protected] http://www.cbc.arizona.edu/xray or http://www.cbc.arizona.edu/facilities/x-ray_diffraction
