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: careinaedgo...@yahoo.com > Subject: [ccp4bb] large R-Rfree difference in "final" structure > To: CCP4BB@JISCMAIL.AC.UK > > 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
