Hi Boaz,
Thank you for your opinions. The resolution is 2.8A and I remembered some
people may think the structure is over-refined when the difference between
Rfree/Rwork is greater than 6.
What do you think the greatest acceptable difference between the two?
Best,
Sun
Boaz Shaanan <[EMAIL PROTECTED]> wrote: Hi,
Why do you think this structure is over-refined ? The Rfree/Rwork difference
of 6.2% seems fine, although you didn't mention resolution. If anything, an
over-refined structure would show a smaller difference, as far as I know. If
all the other criteria (Ramachandran outliers, etc., map) are OK you should
just be happy with your structure.
Cheers,
Boaz
----- Original Message -----
From: Sun Tang <[EMAIL PROTECTED]>
Date: Monday, February 4, 2008 18:41
Subject: [ccp4bb] an over refined structure
To: [email protected]
> Hello All,
>
> I refined a structure with Refmac in CCP4i and the R/Rfree is
> 0.215/0.277. The difference between R and Rfree is too much even
> though I used 0.01 for weighting term in the refinement (the
> default value is 0.3). The RMSD for bond length and bond angle
> is 0.016 A and 1.7 degree.
>
> What may be wrong with the over-refined structure? What is the
> reason for leading to an over-refined structure? How to avoid it?
>
> Best wishes,
>
> Sun Tang
>
>
> ---------------------------------
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Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan
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