> Hello. I am working with drug/DNA complexes. A structure that I have
> been working with has refined to an R of .17 and a free R of .25 with data
> from 8 to 2.25 A. However, with NUCLSQ (a nucleic acid variant of PROLSQ),
> I have very low B values for many non-solvent atoms, with many as low as zero.
> Refinement
> in XPLOR also gave me these low B values though XPLOR doesn't seem to allow
> anything below 2.0. I am at a loss to explain what is going on here. Does
> anyone have an idea?
> --
> Ho Leung Ng
> University of California, Los Angeles
> Molecular Biology Institute / School of Medicine
>ng at tesla.mbi.ucla.edu
Inspect the X-PLOR output file, the overall B factor might had been
refined to be negative.
Check the Wilson plot - your data were probably over-corrected with
an overall temperature factor, i.e., the determined B factor from the wilson plot
might be zero or negative. Try the following (in X-PLOR 3.1),
evaluate ($BW=16.0)
do amplitude (fobs=fobs*exp(-$BW/4*s()^2)
before the B refinement, then see whether the individual B's are reasonable.
Jiansheng Jiang.
