On Mon, Jun 14, 2010 at 1:57 PM, Zhou, Tongqing (NIH/VRC) [E] < tz...@mail.nih.gov> wrote:
> I have some problem in refining a structure. The data goes to 2.4A (with > some 30% completeness at 2.15A), the structure was solved by MR with Phaser, > refinement was done with Phenix, but the r and r-free are now staying at 26% > and 32%, even with all possible waters and missing fragments added. Data was > collected at APS at cryo condition. One thing I noticed during HKL2000 data > processing was that the chi^2 were way too high at lower resolutions shells, > I had to adjust the default error model in HKL2000 to get the chi^2 to > around 1, but this adjustment reduced the overall I/sigI ratio a lot (from > around 20 to 5). > Obvious questions would be: - twinning? - pseudosymmetry? - did you try refining TLS? Not sure about the data processing - how high is "way too high"? I would definitely recommend double-checking the images to make sure the original indexing was correct, e.g. by running labelit.index on them; leaving out spots can definitely result in unreasonably high R-factors without noticeably affecting map quality. -Nat
