Re: [ccp4bb] NCS restraints of domains

- 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: Secondary structure restraints: Oops
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-01-08

Next message:
Subject: Re: Secondary structure restraints: Oops
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-01-08

Subject: Re: NCS restraints of domains
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-01-08

Dear Nick

Using TLS sometimes improves behaviour of NCS restraints (it makes
sense since remaining B values should be similar). However in other
cases it does not improve. Perhaps removal of B value restraints for
these domains may improve NCS restrained refinement. I have not done
tests without B value restraints so I cannot say what would be
behaviour.

I would do several tests before making decision:

1) TLS (as Martyn suggests - domain level) with NCS restraints
2) TLS with NCS restraints without B value NCS
3) NCS without B value restraints

regards
Garib

On 8 Jan 2009, at 10:54, Nicholas Keep wrote:

> I am refining a low (3A) resolution structure of a 3 domain protein.
> There are 4 copies in the ASU. I have been applying tight NCS
> restraints by domain in refmac and have pulled the weak MR solution
> down to Rfree below 30 (just).
>
> However my question is that in 2 of the 4 copies one of the domains
> is very poorly resolved. I can lower Rfree by around 0.5% by
> omitting the domains from the PDB entirely or not applying the NCS
> restraints to these copies of the domain. Clearly they are there
> and should resemble the moderately well resolved copies by
> coordinates but the way Bfactor restraints are applied between NCS
> copies seems to be the issue. If tight restraints are included the
> B factors are much lower (30-40) rather than 60-80 for the poor
> domains.
>
> I was wondering if there is a theoretically correct way to treat this?
>
> Would applying TLS scaling to each domain lead to the residual B
> factors being more balanced?
> Can a B factor offset be applied to the NCS restraints or could I
> only apply a coordinate restraint not a B factor restraint between
> certain copies?
>
> Comments welcomed especially from Garib.
>
> Happy New Year
> Nick
>
>
>
>
>
> --
>
> Dr Nicholas H. Keep
> Dean of Faculty of Science
> Reader in Structural Biology
> School of Crystallography,
> Birkbeck, University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
>
> email n.keep@mail.cryst.bbk.ac.uk
> Telephone 020-7631-6852 (Room G57 Office)
> 020-7631-6868 (Rosalind Franklin Laboratory)
> 020-7631-6800 (Department Office)
> Fax 020-7631-6803
> If you want to access me in person you have to come to the
> crystallography entrance
> and ring me or the department office from the internal phone by the
> door
>

CCP4bb navigation

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

Previous message:
Subject: Re: Secondary structure restraints: Oops
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-01-08

Next message:
Subject: Re: Secondary structure restraints: Oops
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-01-08