Check for translational NCS
And you are way too conservative with resolution. Even those holding
onto the Rmerge-dictated past would probably acquiesce to lower I/sig
cutoff. If you are using aimless, follow its recommendations based on
CC1/2, it's good for you.
Cheers,
Ed.
On Fri, 2013-03-15 at 15:39 -0300, Andrey Nascimento wrote:
> Dear all,
>
> I have collected a good quality dataset of a protein with 64% of
> solvent in P 2 21 21 space group at 1.7A resolution with good
> statistical parameters (values for last shell: Rmerge=0.202;
> I/Isig.=4.4; Complet.=93% Redun.=2.4, the overall values are better
> than last shell). The structure solution with molecular replacement
> goes well, the map quality at the protein chain is very good, but in
> the final of refinement, after addition of a lot of waters and other
> solvent molecules, TLS refinement, etc. ... the Rfree is a quite high
> yet, considering this resolution (1.77A).(Rfree= 0.29966 and Rfactor=
> 0.25534). Moreover, I reprocess the data in a lower symmetry space
> group (P21), but I got the same problem, and I tried all possible
> space groups for P222, but with other screw axis I can not even solve
> the structure.
>
> A strange thing in the structure are the large solvent channels with a
> lot of electron density positive peaks!? I usually did not see too
> many peaks in the solvent channel like this. This peaks are the only
> reason for these high R's in refinement that I can find. But, why are
> there too many peaks in the solvent channel???
>
> I put a .pdf file (ccp4bb_maps.pdf) with some more information and map
> figures in this
> link: https://dl.dropbox.com/u/16221126/ccp4bb_maps.pdf
>
>
> Do someone have an explanation or solution for this?
>
>
>
> Cheers,
>
> Andrey
>
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
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When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
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