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CCP4MG  May 2009

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Subject:

Problem with Rfree and Rfac

From:

Sravanti <[log in to unmask]>

Reply-To:

Mailing list for users and developers of CCP4mg <[log in to unmask]>

Date:

Wed, 20 May 2009 15:41:12 +0100

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text/plain

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text/plain (33 lines)

Hello CCP4i GURUs,

I am working on a 3A resolution structure and I recently got a solution from
Phaser. I have just started building and refining the structure. I started
with Rfree-43 , R-41.7 and the first round of building and refining gave me
Rfree- 40 and Rfac- 35.5. The Rfree and R do not decrease to the same extent
during refinement (Refmac5). Further rounds of refinement increases the
difference between R and Rfree (Rfree-38 Rfac- 30)

I am worried that since this is just the beginning further rounds of
building and refinement might drastically increase the gap between R and
Rfree. On the positive note the FOM is increasing with refinement and the
maps look better. I also see new density at several regions where I can
build into.

I tried to change the weighting factor and geometric parameters after I read
the earlier posts here. The references noted earlier were extremely helpful.
Here are some other details of my structure which might help you

Space group- P1 21 1
Resolution- 3A
Solvent content- 39%
unit cell parameters- 63.3,  90.72 , 86.11, angles-  90, 91.5 , 90 

Please enlighten me with your suggestions. Is it fine to go ahead with this
refinement or is there a way I can reduce this difference between R and Rfree??

Your help will be greatly appreciated. As this is my first structure I am
excited about it!!!

Thank you

Sravanti

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