Auftrag von *??
*Gesendet:* Mittwoch, 26. Juni 2013 06:05
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [ccp4bb] Rfree is 20%,why still green and red density?
Hi everyone,
I now meet some problems when trying to solve structure.Space
group is P6422, and Mathews function shows
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Rfree is 20%,why still green and red density?
Hi everyone,
I now meet some problems when trying to solve structure.Space group is P6422,
and Mathews function shows there are 4 molecules in one asymmetry unit.
However, Phenix-autobuild shows only 2
The Matthews function is based on an average protein crystal with 50%
solvent.
Not sure what that a 'Matthews function' exactly would be - and that an
assumption of 50 solvent
content is made anywhere in the Vm calculation is new to me. The only
defensible
prior that goes into the
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Dear Jiang Yan,
how many reflections to you have in the free-set. At P6422 with a
resolution of 2.8 you may have only a few hundred and thus not get a
reliable Rfree value. Its low value may be due to overfitting.
What does the cyrstal packing look
you may have only a few hundred and thus not get a reliable Rfree value.
The estimate for the error in R free as a function of the number of
reflections is as follows:
Brunger initially estimated^35 that the uncertainty in R-free is
proportional to
(Nref )^-1/2, which is reasonable to assume
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Sure, but in P6422 with 2.8A I'd say that 5% of reflections are more
likely near 40-50 than 'a few hundreds' if the cell too small. And
most people simply flag 5% of their reflections without checking how
many these really are. Splitting these up into
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Bernhard Rupp
Sent: Wednesday, June 26, 2013 13:31
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfree is 20%,why still green and red density?
you may have only a few hundred and thus not get a reliable Rfree value.
The estimate for the error in R
Hi everyone,
I now meet some problems when trying to solve structure.Space group is P6422,
and Mathews function shows there are 4 molecules in one asymmetry unit.
However, Phenix-autobuild shows only 2 molecules in on one asymmetry unit,
after refinement, Rfree=20%,(resolution is 2.8A).