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: [log in to unmask]
>> Subject: [ccp4bb] large R-Rfree difference in "final" structure
>> To: [log in to unmask]
>>
>> 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
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