Hi Mandar,
Thanks for the clarification. Eleanor (and others) who assumed the reported
statistics were for the overall dataset were spot-on and my assumption was
incorrect. As Eleanor previously stated, since those statistics were for
the high resolution shell, they’re reasonable.
As for whether
Hi Mandar Bhutkar,
ok now that new table shows that your data are at least reasonable.
Nevertheless it pays off to optimize the data processing, and the high
resolution cutoff ...
Is it publishable? Not possible to say from your table. If I were a reviewer,
I'd want to see the raw data and
We should all thank you mandar for stimulating our thinking and setting off
a thoughtful discussion!
This is perfectly publishable - st 2,6A placing water molecules is a bit
problematic and you will probably only see clearly the well ordered solvent
hence the lower average b factor.
Just a
This is why I said this is somewhat subjective.
I would agree I/sigI of 0.6+ and cc1/2 of 0.5+
in high res shell is fine but these values are overall, as the resolution
range is 23-2.6 angstroms.
On Thu, Nov 2, 2023 at 12:16 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Am I confused? I would accept an I/SigI of 1+, and a CC1/2 of 0.5 as pretty
acceptable?
E
On Thu, 2 Nov 2023 at 15:03, Dr. Kevin M Jude wrote:
> As suggested by the (conflicting) observations of Eleanor and Nicholas,
> it’s not clear whether you are showing data collection statistics for the
>
Hi Mandar Bhutkar,
the data statistics (Rmerge, I/sigma, CC1/2) appear to be poor.
So you may want to check the data processing; try with different programs, and
perhaps with help from experienced people in your group.
You could ask for help here, but you should give more details - what
As suggested by the (conflicting) observations of Eleanor and Nicholas, it’s
not clear whether you are showing data collection statistics for the full
resolution range or just for the high resolution shell. If for the whole
dataset, your Rmerge, I/sigma, and CC1/2 are high, low, and low,
Mandar,
It would also be helpful if you could share the statistics in the highest
resolution shell. But to me (which is admittedly a bit subjective), as
noted by Eleanor, the R-merge seems a bit high and the your I/sigma and
CC1/2 seem a bit low. Which doesn’t really matter if you can build a
Well - you probably could use data to a higher resolution I/SigI and CC
1/2 are quite high.
The better the resolution the better the model usually.
On the other hand your Rmerge is high-ish. Hard to comment without seeing
the data processing results. Look at the plots of 2nd moment, wilson plot,
Dear Mandar,
- you may be able to find some more, less well-ordered, waters by looking at
(difference) maps. These will probably refine to have higher B-factors, pushing
your average up.
- some of your best-ordered water molecules may in fact be metal ions, you can
check the coordination.
Hi everyone,
I am working on one of the x-ray diffraction data. Refinement details are
given below. My solvent b factor is 18.44. Can anyone pls suggest me how to
improve the data?
Thank you.
--
Mr. Mandar Bhutkar,
Ph.D. student,
Molecular Virology lab,
IIT Roorkee.
Resolution range
23.06–2.60
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