Why the Rfree value is lower than Rwork?
在 2010年7月19日 上午3:41，孙庆祥 写道：
> Dear Collins and all,
>
> Thanks for the reply. Please find the following pdb header. For your
> information, this is after refmac5 with twin-refinement option selected.
> This is the best R values that I'm getting. Cutting re
Your beta and gamma angle in P1 are awfully close to 90 degrees. Are you sure
about P1 ?
Could it be C2 with beta of 104 ˚ ? I'm assuming the CRYST card below belongs
to your structure right ?
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Mol
Hi, Collins,
Thanks for the valuable comments.
I tried refineing using 2.0A cutoff, but the problem persists. (No Molrep
solution is found with R less than 0.7, ).
Could you please show me how can I indentify and eliminate the catastrophic
error that I'm having with the data?
Regards,
Hi,
This is a case of small protein packed in P1. One question may be
raised if you have all molecules added to your model? Based on the
cell constants and the information of ~60 residues you provided, the
solvent content is ~70%, which is not that normal for a small unit
cell (18 Å or
I would be careful with Rfactors at the early stages of refinement,
especially in the presence of twinning (apparent or real). You can see
weird behaviour of Rfactors in this presentation:
www.ysbl.york.ac.uk/refmac/Presentations/Refmac_Erice_workshop.ppt,
slides 18-20.
In short if you have
Hi Jeremy,
Just looking at the stats:
1- you could try to remove the low intensity reflections (are they
reflections, or are they just indices - it's difficult to say), i.e. the
first 4 shells in your tables dealing with intensities;
2 - you could try to truncate the high resolution to 1.6 A.
Dear Collins and all,
Thanks for the reply. Please find the following pdb header. For your
information, this is after refmac5 with twin-refinement option selected. This
is the best R values that I'm getting. Cutting resolution does not help much in
getting the Rs down...
HEADERSWISS-M
Given your unit cell parameters + high Rsym I'd say you have an indexing
problem. If you try P2, what happens? I suspect that you might have
something as simple as incorrect beam center position and while
integration works, scaling fails (the only way you are getting away with
it is by choosing P
Have you used pointless to examine possible spacegroups? It is possible
to get one lattice point out and get a very high rsym
pointless will check these possibilities for you
The cell could be this:
C m m m 39.6 149.9 18.2 89.9 90.0 90.0 0.10 [-k,-k-2l,h]
You need to go back to the
You mention that your Rsym is 0.6 - this seems outrageously high (except if the
0.6 is just for your outer resolution bin). If 0.6 is indeed the overall Rsym
you have a basic problem of unit cell and space group assignment to reconsider.
Check if your processing accounts for all spots and check
> Rsym is 0.6
I'd be seriously worried about this. An R-sym value of 0.6 in the entire
resolution range (I assume) means that your
reflection intensities do not match. This is the value of the Rsym I could
expect in the high resolution bin - in
the age of maximum likelihood refinement, not in
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