With such good data you would expect lower R factors I agree.
I use all the COOT validation tools - Ramachandran, diff map peaks etc
to try to pinpoint errors.
Also anomalous difference maps hoping to verify S positions and check
the sequence fitting.
You could let Arp/Warp rebuild it from t
How does the Molprobity report look like ?
How many Rama outlieres, bad Cbeta, rotamers ?
What's your percentile ?
Look at the multicriterion chart to fix your problems :-)
http://molprobity.biochem.duke.edu/
Juergen
Yongchao Li wrote:
Dear all,
Thanks for all replies.
After water addition,
Dear all,
Thanks for all replies.
After water addition, R work is 0.27 and R free 0.33.
TLS and NCS results no significant approve.
Space group seem right, other space group like P21212 is worse.
>From truncate result, it is not twinning.
More detail is below:
space group P212121 a=150.099 b=148.
Have you tried TLS and NCS? Maybe these can lower the R free a little.
But ,the quality of your model depends on the quality of your data and
completeness of your model etc.
Yongchao Li wrote:
I have a large molecule to refine.There are about three thousand
residues in one asymmetric unit. Ex
Yongchao Li wrote:
I have a large molecule to refine.There are about three thousand residues in one asymmetric unit.
Except for the lack of electron densities in several places, where the
loops have been deleted, the rest parts fits well with density. But the R free and R work are all beyond 0.
kholm, Sweden
___
- Original Message -
From: Yongchao Li <[EMAIL PROTECTED]>
Date: Tuesday, January 8, 2008 1:51 am
Subject: [ccp4bb] How to refine large moleculars?
To: CCP4BB@JISCMAIL.AC.UK
> I have a large molecule to refine.There are about three thousand
> residues in one asymm
Depending on your data quality and the nature of the crystal it might be
that you cannot reduce R/Rfree any further.
Low R/Rfree is not the goal of refinement and model building - at least
not for the humans doing it. The goal is to get as good a model as
possible, and if your data are not very
I have a large molecule to refine.There are about three thousand residues in
one asymmetric unit.
Except for the lack of electron densities in several places, where the
loops have been deleted, the rest parts fits well with density. But the R free
and R work are all beyond 0.30 (R free = 0.35,
