Hi Careina,
in our lab we once had the problem, that the asymmetric unit contained 8
molecules,
whereas 7 had only been modeled. Somehow the 8th monomer had evaded
detection.
So be careful not to miss density.
Matthias
On 7/13/2011 7:54 PM, Robbie Joosten wrote:
Hi Careina,
Assuming you don't suffer from a very poor data parameter ratio that would lead
to such a large R-free/R, you need to improve your refinement. If you have NCS
you should use local NCS restraints. You could also try jelly-body restraints,
although they may not work at your resolution.
Cheers,
Robbie
________________________________
Date: Wed, 13 Jul 2011 08:38:38 -0700
From: [email protected]
Subject: [ccp4bb] large R-Rfree difference in "final" structure
To: [email protected]
Dear ccp4 bulletin board
I just have a slight concern regarding my Rwork Rfree difference. I
have a structure that I have solved. I am reasonably content that it is
complete because it has refined well, it no longer has bad geometries
and contacts and all the rotamers, ramachandra, bond lengths etc are
good. It gives favourable scores on molprobity and procheck. My only
concern is the R factor difference. The resolution of the structure is
2.3A. The R factor is 0.24 after refinement but the Rfree is 0.33 which
seems to me to be rather high. Should I be concerned?
During refinement Rfree only drops from about 0.36 to 0.33 while the R
factor drops from 0.31 to 0.24.. I have removed automatic weighting in
refmac in order to constrain my bond lengths and angles during a couple
of rounds of refinement. This did not have any effect on the R factors,
however. I am fairly content that the space group I have chosen is
correct so I am not sure what else could cause the big difference in R
factors? There is no twinning.
Can I be satisfied that my structure is correct despite the high R free
or should I be doing other checks/ trying other things before I can
submit this structure?
Thank you for any help
Careina
