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Oops oops...Oops oops oops....
Typo... fat fingers....!
Rfactor and Rfree values were 21.9% and 24.3% (NOT 22.4%) respectively
PDB ID: 1S32
Thanks Ian!
Raji
Ian Tickle wrote:
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Isn't such a small difference Rfree - Rwork (i.e. 0.5%) rather
improbable at that resolution?
-- Ian
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Raji Edayathumangalam
Sent: 08 November 2006 17:25
To: Yi Xue
Cc: [email protected]
Subject: Re: [ccp4bb]: missing residues and R
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In one of my structures at 2 Ang resolution , the final
Rfactor and Rfree values were 21.9% and 22.4% respectively. I
had ~18-19% total protein missing in the final model. All of
this missing protein is completely disordered in all
nucleosome structures known to date and likely have no or
insignificant effect on the Rfactor and Rfree. The final
model also had a lot else accounted for, namely, 100% of the
DNA, ~900 water molecules, lots of ions and a ligand.
But had I omitted, say, 18-19% of structured helices from the
protein model, the Rfactor and Rfree would increase
significantly. Then, if I continued to refine without
accounting for most of the model or without improving the
model in any manner, I could expect to see an artificial
lowering of the Rfactor without any further decrease in the
Rfree and a resulting increase in the difference between the
Rfactor and the Rfree.
I don't know what the nature of your 'missing residues' is.
HTH.
Raji
Yi Xue wrote:
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Hi, all:
If for a small protein, about 10% residues missing, will it
affect the final R and Rfree?
If yes, how serious will it be?
thanks
Yi
--
Raji Edayathumangalam
Postdoctoral Fellow
The Rockefeller University
Box 224. 1230 York Avenue
New York, NY 10021
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Raji Edayathumangalam
Postdoctoral Fellow
The Rockefeller University
Box 224. 1230 York Avenue
New York, NY 10021
