Dear Careina,
As other have mentioned, my feeling is that something is suspicious.
However the problem might be very difficult or impossible to catch and
other structures have been deposited with similar R/Rfrees...
What I would check in addition to what has been mentioned, is if some
twinning is present. With say a twin-factor of 10-20% processing may
proceed sort of ok and refinement as well with a somewhat higher Rfree.
You may also suffer from disorder. You mention that you model is
complete: does that mean that the complete sequence of your protein has
been fitted, or does this mean that no more positive difference density
is left? If a significant portion of your protein is not visible, this
may still compromise your Rfactors. In the latter case, I don't think
you can do much about it, except offering this as an explanation for
your high R/Rfree.
Best,
Herman
________________________________
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Careina Edgooms
Sent: Wednesday, July 13, 2011 5:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] large R-Rfree difference in "final" structure
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
