Re: [ccp4bb] Rfree and unaccounted density

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Li ion scattering factor
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-04

Next message:
Subject: University of Auckland - Lecturer in Structural Biology
From: Charles Ballard c {- dot -} c {- dot -} ballard {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-09-05

Subject: Re: Rfree and unaccounted density
From: Ranvir Singh rsvatsa {- at -} YAHOO {- dot -} COM
Date: 2007-09-05

Dear Vineet
Following points shall be kept in mind.
1.If you have been able to model most of the protein
into the electron density, then its a bit strange.
your refinement parameters suggest that refinement is
still away from convergence.
2.You might be trapped in local minima, and in this
case simulated annealing might help you.
3. As far as picking waters, to me, its perhaps a bit
early to pick water at this satge of refinement.
4.Also, you can look at ramachandran plot to see which
residues needs attention.
5.Something might have co-crystallized along with your
protein. You can check your crystallization
conditions.
Ranvir

--- Vineet Gaur wrote:

> Hi all
>
> i m solving a structure at 2.2 A using MIR. rt now
> my Rfree is 30.55% and
> Rcryst is 28.51%. i have already carried out B
> factor refinement n water has
> also been picked up to 2.3 sigma cut off. now i m
> not able to refine the
> structure any further.
>
> The protein has been purified directly from the
> source. At this pt of
> refinement i m able to see lot of unaccounted
> densities, far bigger to b
> accounted by water or sugar, as we don't have any
> information abt the
> possible molecules that can interact with this
> protein.
> .
> is this unaccounted density be the reason why i m
> not able to refine the
> strucure?
>
> thanx in advance
>
> Vineet Gaur
>

____________________________________________________________________________________
Got a little couch potato?
Check out fun summer activities for kids.
http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Li ion scattering factor
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-04

Next message:
Subject: University of Auckland - Lecturer in Structural Biology
From: Charles Ballard c {- dot -} c {- dot -} ballard {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-09-05