No comments on much of your message but I cannot believe you can get better
results by cutting anisotropic 2.1A data to 3.3A!!
You MUST be throwing away valuable experimental information,, remember
crystallography is not about getting low R factors but about getting a
model consistent with your experiment.
eleanor
On Mar 5 2012, Rajesh kumar wrote:
Dear All, Thanks for all the suggestion. Data is anisotropic. Since
anisotropic correction with the UCLA server didnt give any good
Molprobity scores and didnt reduce the R/Rfree at 2.1A, I am using ~3.3A
data for further refinement. Using Tom's suggestion of target restrains
reduced the gap brtween R/Rfee to with in 5%. I haven't tried Pavel'
suggestion but when I do I will post the results. I used a 2.3 A MR model
as target to get R/Rfree 0.2209/0.2597. When I used coot real space
refine zone to fix few molprobity outliers, most of the favored residues
become outliers. Almost all residues changed to become outliers. I am
wondering why all the residues are moving from favored to outlier regions
after restrained refinement. I thought all the residues would be fixed
(fit) to the map and wouldn't change during the coot exercise, and this
is what I see in the 2.3 A target/model structure ( with R/Rfree
0.1693/0.1961). I don't know if is this common for a low resolution or I
didn't understand this whole thing of refinement correctly. Thanks for
all the help, Regards,Raj
Date: Sun, 4 Mar 2012 21:02:51 +0000
From: eleanor.dod...@york.ac.uk
Subject: Re: [ccp4bb] sudden drop in R/Rfree
To: CCP4BB@JISCMAIL.AC.UK
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
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
