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The B-factors for the two different strands of DNA in nucleosome
structures fluctuate with about a 10-bp periodicity all along the length
of the 146-bp DNA. The strand that faces protein has much lower
B-factors in stark contrast to the strand that faces the solvent. The
minimum-to-maximum range for B-factors reported in literature for
nucleosomal DNA are from 40-140 (incl. different programs, different
scientists, different labs).
One of the DNA-specific polyamide ligands I worked with was bound to a
stretch of DNA with B-factor around 140. There was unambiguous
difference density for the ligand subsequent to molecular replacement.
The ligand has sub-nanomolar affinity for its target sequence and all
possible biochemical assays provided unequivocal evidence for bound
ligand. There was not much else to do except to model the ligand and to
refrain from over-interpreting the density.
Just my example.
Raji
Becker, Joseph W wrote:
The data may be telling you something. Less than 100% occupancy is
not unheard of.
Joe Becker
------------------------------------------------------------------------
*From:* [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] *On
Behalf Of *michael nelson
*Sent:* Friday, January 05, 2007 1:55 PM
*To:* ccp4bb@dl.ac.uk
*Subject:* [ccp4bb]: ligand refinement
Hi,all:
During water-tidy, I found a big bulb of density in my active
site(only a bit in 2Fo-Fc map but quite big in Fo-Fc above 3.5sigma
level).This looks pretty much like my ligand. Then I put it in and
start refinement, but the program always give a high B-factor for this
ligand(above 100).From the difference map, I'm convinced I have the
ligand there but how to get it refined with a reasonable
B-factor?Please advise.
Mike
--
Raji Edayathumangalam
Postdoctoral Fellow
The Rockefeller University
Box 224. 1230 York Avenue
New York, NY 10021
