Re: [ccp4bb]: R and Rfree factor for 2.0 A model

[Brad Bennett]

Hi Mousheng

 So, since this is the CCP4 bulletin board, I'll say it: the million dollar question is have you simply tried switching to refinement in Refmac? You can perform restrained refinement and increase the sigma weighting value to relax the restraints imposed on your model by the libraries. At 2A resolution, you may be able to push this well above the default value (I think it's 0.3). Of course, check the output rmsds and make sure they're "reasonable." (For discussion on that, see the last few days on the CCP4 bull. board)

 One other thing: check an Fo-Fc map at >+3 sig to make sure you've modeled everything. I suppose you could have a metal or a glycerol (or something else in your purification or crystallization solutions) that still needs to be added? Of course, also check a map at negative sigma to make sure you most every atom is happy...

 

HTH

Brad

--
Brad C Bennett
Postdoctoral Research Assistant
Department of Biochemistry,
Cellular and Molecular Biology
(BCMB)
University of Tennessee-Knoxville
865-974-3045
[EMAIL PROTECTED]

-------------- Original message from "Wu Mousheng" <[EMAIL PROTECTED]>: --------------

Dear all,

 

I am refining my model with 2.0A using CNS. I have fitted most of the protein sequence into the model (150 of 160 aa). I also added 100 water molecules into the model. The final R and Rfree factor are about 26% and 28%, respectively. I am wondering why I can not refine my model to low R and Rfree factors below 25%.  The geometry of my final model is very good. 96% residues are in most favorable region.

 

I think my data is quite good. I/sigma(unaverage) and completeness at highest resolution shell is 2.3 and 99%. Rmerge is about 6%. Redundancy is about 5.

 

Is my model acceptable based on the R and Rfree factors? Is there any reason for the high R and Rfree factors?

 

Thanks!

 

Best,

Mousheng Wu,

Institute of Molecular and Cell Biology, Singapore

 

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