Dear All,
Sorry for the wrong pointless file. With this mail i have attached the
pointless run file from the unmerged data. This file also suggests the
C2221 spacegroup.
Appu
On 22 April 2015 at 17:40, Christian Roth wrote:
> Hi Appu,
>
> you start already with a fixed spacegroup (scaled merged
Hi Appu,
you start already with a fixed spacegroup (scaled merged data) according
to your pointless log. So you can't get another possible solution from
pointless.
Cheers
Am 22.04.2015 um 22:28 schrieb Appu kumar:
Dear CCP4 Member,
I seek your advice on the refinement issues at the low res
The Xtriage & Pointless logs don't show definitively that the space group is
C2221 as they have been run on the merged data. You may need to check them with
the unmerged data, and perhaps run molecular replacement in a lower symmetry
such as C2
Phil
On 22 Apr 2015, at 22:28, Appu kumar wrote:
Dear CCP4 Member,
I seek your advice on the refinement issues at the low resolution 4A. I am
trying to refine a membrane protein structure after getting the phases from
MR using the PHASER. The soluble domain structure which comprises of 40% of
protein has been used as template (sequence identity 8
If your protease depends on an oxyanion hole for stabilizing the
transition state, fluoride ions are known to be a potent inhibitor of
these proteases. (It is a quasi-diagnostic test for serine-type
proteases, and related cysteine proteases.) This might allow you to get
reactant bound without c
Hi Dipkar,
My understanding is that the majority of a protease's activity comes from the
oxyanion hole activating the scissile bond. Mutating the nucleophile reduces
activity, sometimes appreciably, but does not kill the enzyme. Were your
SDS-PAGE experiments on the same time scale and buffer c
We had a similar situation with a catalytically dead serine protease.
Initially I was excited to think we might be seeing residual catalytic activity
of the mutant enzyme on a highly specific substrate; however, the activity
turned out to result from contamination with a very small amount of wt
hello Dipankar,
Your queries have generated much interest. It would be helpful if you told
us which clan the cysteine
peptidase you are working with is from. Also it would be very helpful if
you could show us the
electron density of the "cleaved" peptide in the active site. One presumes
that you ha
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Hash: SHA1
Thanks for all the help!
We will restart the job with the KILL option as Jens suggested.
We will also send a copy of the Phaser log file to Randy. This is
not a case of Phaser simply trying harder - it is doing the same
search over and over
Dear Dale,
as George points out, you may be interested in trying ARCIMBOLDO, as it has
been successfully applied to coiled coil proteins recently, as in the case
of
Franke et al (2014) Open Biology, 4. p. 130172 or Sammito et al (2013)
Nature Methods 10: 1099-1101 . Different models can be searc
Dear Dale,
This is a known issue with AMPLE and will be fixed with the next release.
In the meantime you can tell AMPLE to pass the KILL option that Randy mentions
to PHASER, by adding the following arguments to your script:
-mr_keys PKEY KILL TIME 360
this will kill PHASER after 360 minutes (
Hi Dale,
It must actually be AMPLE deciding how many copies to search for. Phaser will
give you some information about how consistent the specified composition is
with the Matthews volume, but it just searches for the number of copies that
it's instructed to look for. We haven't put the intel
Dear Dale,
Isabel Uson's ARCIMBOLDO-LITE works well for coiled coils and has the
same resolution
requirements (2.1A or better) as AMPLE because both use SHELXE to expand
the solution.
It also employs PHASER to place a small fragment but it is often
sufficient to let it search for
just two or
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