Re: [ccp4bb] difference of R work and R free as a function of resolution

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: difference of R work and R free as a function of resolution
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2007-11-15

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Subject: Reindex and Rfree column
From: Florian Schmitzberger Florian {- dot -} Schmitzberger {- at -} KI {- dot -} SE
Date: 2007-11-15

Subject: Re: difference of R work and R free as a function of resolution
From: "Miller, Mitchell D {- dot -} " mmiller {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-11-15

Have a look at

Rfree and the Rfree Ratio. I. Derivation of Expected Values of
Cross-Validation Residuals Used in Macromolecular Least-Squares
Refinement. Tickle IJ, Laskowski RA and Moss DS
Acta Cryst. (1998). D54, 547-557
http://dx.doi.org/10.1107/S0907444997013875

and

Rfree and the Rfree ratio. II. Calculation of the expected values and
variances of cross-validation statistics in macromolecular least-squares
refinement. Tickle IJ, Laskowski RA and Moss DS Acta Cryst. (2000). D56,
442-450 http://dx.doi.org/10.1107/S0907444999016868

Regards,
Mitch

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs
Sent: Thursday, November 15, 2007 8:42 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] difference of R_work and R_free as a function of resolution

Dear crystallographers,

today I explained to a student that I believe that the difference of
R_work and R_free should decrease as a function of resolution, because
at high resolution there is less danger of overfitting, whereas at low
resolution one is always overfitting to some extent. I'd say this should
be true at least in absolute terms, but probably even in relative terms:
for example, for a 1.5A structure I'd expect R_work/R_free= 14%/16%,
whereas at 3A I'd expect 28%/35%.

I believe that I saw plots (maybe in a link given in a posting on
CCP4BB) obtained for structures from the PDB, which confirmed this
hypothesis. But I've been googling and searching through postings now
for quite some while, and cannot seem to find anything to that effect.

Does anybody have a pointer to an analysis of this effect?

thanks,

Kay

P.S. Would be good to put this into the CCP4 Wiki article on R-factors
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: difference of R work and R free as a function of resolution
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2007-11-15

Next message:
Subject: Reindex and Rfree column
From: Florian Schmitzberger Florian {- dot -} Schmitzberger {- at -} KI {- dot -} SE
Date: 2007-11-15