V.Y. Lunin, P.V. Afonine & A.G. Urzhumtsev. (2002). Acta Cryst., A58, 270-282.
Afonine P.V. (2002). CCP4 Newsletter on Protein Crystallography. 41.
I'm sure a few mins of googling gives you a whole bunch of other publications related to this.
Cheers,
Pavel.
On 11/8/06, Ian Tickle <[EMAIL PROTECTED]> 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
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> 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:
> > *** For details on how to be removed from this list visit the ***
> > *** CCP4 home page http://www.ccp4.ac.uk ***
> >
> >
> > 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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