Hi,
I found that my protein bound ethidium bromide in an agarose gel. I tested that
by treating my protein with protease and DNAse in two different tubes and
running a gel. The band in the agarose gel disappeared only when the
protein was treated with protease. It is worth trying.
I hope that
If both the PDB and mtz for the pdb have been assigned to P1 space group for
some reason, can this lead to Rwork higher than Rfree during refinement?
If after converting my PDB and mtz to P1 space group, and I have forgotten what
is the original space group for my PDB and mtz before
Dear Wolfram,
I have a perhaps optimistic view of the effect of high-order NCS
on Rfree, in the sense that I don't view it as a problem. People
have agonised to extreme degrees over the difficulty of choosing a
free set of reflections that would produce the expected gap between
Rwork and
Hi Wolfram,
You didn’t tell us where your model came from but 10 cycles of TLS and 10
cycles of restrained refinement is not enough for a refinement to converge if
you just picked your test set. Try resetting your B-factor and doing 30-40
cycles refinement in REFMAC.
Cheers,
Robbie
I suppose if I was the referee for this structure and your FreeR is so
close to the Rfactor I would ask you to ensure you had the right space
group - is the 6 fold NCS actually 2 fold NCS with a crystallographic 3
fold..
Cases occur where R32 is indexed as C2..
Certainly if the Rfree set is
Regarding what Eleanor said:
The program “labelit,” available within Phenix from command line, can check
automatically for higher space groups.
In the labelit documentation/homepage it mentions the command:
labelit.check_pdb_symmetry [pdb coordinate file] [data=mtz file]
JPK
From: CCP4
Hello,
my question concerns refinement of a structure with 6-fold NCS (local
automatic restraints in REFMAC) against 2.8 A data. The size of my free set
is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to
4.3 % of reflections.
A refmac run of 10 cycles of TLS and 10 cycles of
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