Presumably your data is quite anisotropic, and low resolution, so it is
quite likely that a TLS model will give much better description of the B
factors than more classical refinement.
Modelling solvent at that resolotion will be tricky of course.
Elesnor
On Mar 4 2012, Joseph Cockburn wrote:
Hi Rajesh,
If you're seeing a lot of extra density coming up in the map in regions
where you previously added waters, is it possible that this extra density
corresponds to a part of your protein that you previously thought was
disordered and is thus missing from the current model? At this resolution
you wouldn't expect to see many waters.
Also, to the best of my knowledge, the relative weighting of the X-ray and
geometry terms in BUSTER is set by the program so as to produce a rmsd in
bond lengths equal to a target value. The default value of this is 0.01
Ang (I think) but you can change this using the -r option on the command
line. Using a lower value will reduce the weight on the X-ray term and may
lower the R/R-free gap.
Best wishes,
Joe
Dear All, I have a 3.3 A data for a protein whose SG is P6522. Model
used was wild type structure of same protein at 2.3 A. After molecular
replacement, first three rounds of refinement the R/Rf was 26/32.8,
27.1/31.72 % and 7.35/30.88 % respectively.In the fourth round I refined
with TLS and NCS abd added water and the R/Rf dropped to 19.34/26.46. It
has almost 7% difference. I also see lot of unanswerable density in the
map where lot of waters were placed. Model fits to the map like a low
resolution data with most of side chains don't have best density. I was
not expecting such a sudden drop in the R/Rfree and a difference is
7.2%. I am wondering if I am in right direction. I am not sure if this
usual for 3.3A data or in general any data if we consider the
difference. I appreciate your valuable suggestions. ThanksRaj
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
