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
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