thanks to all for useful comments!
one more thing:
Brunger (1997, Meth Enzymol 277:366-396) estimates the uncertainty in
Rfree as 1/sqrt(n), where n is the number of reflexions used for
calculating Rfree. So 1500 refs would be an estimated error of 2.5% in
Rfree, which I would consider acceptable.
Fig. 1 of the paper cited below nicely illustrates how putting more
refs in Rfree makes de rms of the refined structure larger, i.e. leads
to a more inaccurate structure.
Greetings,
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
On 16 Jun 2008, at 21:06, Michael S. Chapman wrote:
Mark et al.
Rfree can be calculated with as few as 150 reflections, depending on
the
desired precision of Rfree.
The real issue is scaling. Many programs scale vs. the test set
independently, which becomes unstable with a small test set, and
this is the
main cause of error in Rfree. The topic and remedy are discussed in:
Chen, Z., E. Blanc, et al. (1999). "Improved free R-factors for the
cross-validation of structures." Acta Crystallographica D55: 219-24.
Good luck. Michael.
Michael S. Chapman, R.T. Jones Professor of Structural Biology
Dept. Biochemistry & Molecular Biology; School of Medicine, Mail
Code L224
Oregon Health & Science University
3181 Sam Jackson Park Road; Portland, OR 97239-3098
[EMAIL PROTECTED] / (503) 494-1025; http://xtal.ohsu.edu/
-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Mark J. van Raaij
Sent: Monday, June 16, 2008 11:22 AM
To: [email protected]
Subject: [ccp4bb] How many reflections for Rfree?
Dear All,
It has recently been put to me that 5-10% of reflections should
always
be set aside for calculation of Rfree. However, when one has, say,
200
000 reflections (high resolution and/or large asymmetric unit), that
seems to me to be a waste, because it would mean removing 10 000 to
20
000 reflections from the refinement target.
My opinion is based on discussions with a particular knowledgeable
crystallographer and a meeting report (
http://journals.iucr.org/d/issues/1996/01/00/li0216/li0216.pdf
), in which 1000 reflections is said to be enough (i.e.
statistically valid). As a result, I always take 1000-1500
reflections, independently of the number of total reflections,
adjusting the percentage or the width of the thin shells (in case of
NCS) accordingly.
What is the opinion of the community? And, if you agree with me, how
should we try to get this opinion (more) generally accepted?
On a related note, how to refine a structure with only 5000
reflections, which could happen when you have a small a.u. and modest
resolution? Could, exceptionally, a lower absolute amount of
reflections be used for Rfree, say 500?
Greetings,
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
