Sounds like a good candidate for (domain-level) TLS to me.
Cheers
Martyn
-----Original Message-----
From: CCP4 bulletin board on behalf of Nicholas Keep
Sent: Thu 1/8/2009 10:54 AM
To: [log in to unmask]
Subject: [ccp4bb] NCS restraints of domains
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 [log in to unmask]
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
