Christine,
As interesting as the di-Tyrosine idea is, from the picture you
provided, it looks more like the two tyrosines share a C=C bond.
Given your slightly elevated R-factors and the high symmetry space
group, I would thoroughly check for even the slightest sign of twinning.
I once had
googling dityrosine suggests thaey can be formed by osidation by Cu or Ni
ions.
In structures of cytochrome oxidase, Tyrosine forms a covalent bond
from the same meta carbon to NE2 of a histidine. see Fig 1 of:
http://www.sciencemag.org/content/280/5370/1723.long
And histidine is ligating a
Dear ccp4 users,
I tried to install CNS under Debian 64bit. I followed the installation
giude as reported by CNS developers but I received the following
message when souurcing cns_solve_env:
bash: setenv: command not found
bash: setenv: command not found
bash: cns_solve_env: line 32:
Hi Jan,
I wonder if the protein has a hexaHis tag. I recently was working on a Fe-S
containing protein and noticed significant aggregation/precipitation. After I
cleaving the His tag, the enzyme seems stable for days in the same buffer.
HTH,
Yuri
Hi Fulvio
Your scripts are for csh (or tcsh) so won't work under bash. Have you
checked whether there are versions for sh (or bash) already set up?
If not you will have to run them under csh, or better still tcsh.
If the script doesn't work with the version of csh or tcsh you are
using you
Dear Fulvio Saccoccia,
along the lines of Ian Tickle's reply: there should be a script
cns_solve_env_sh using /bin/sh, which is usually a soft-link to
/bin/bash. I use this script for setup of CNS under bash.
Best regards,
Dirk.
Am 12.07.12 16:49, schrieb fulvio saccoccia:
Dear ccp4
Hi Jim,
25% is w/v. Thanks for the information. Will check the webinar.
Thanks,Min
From: jim.pflugr...@rigaku.com
To: mzhang...@hotmail.com; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] cryo for high salt crystal
Date: Tue, 10 Jul 2012 17:39:56 +
Sucrose, sorbitol, Splenda, trehalose,
We frequently crystallize one of our proteins and variants of it in
1.6-1.8 M ammonium sulfate solutions. Cryoprotection with 25-30%
glycerol or 25-30% glucose does not cause precipitation of salts. Both
KCl (4.6 M) and ammonium sulfate (5.6 M) have enormous solubilities in
water, so I would
Roger's note reminded me of some older literature (old in the sense that this
problem extends back into the mid-1970's). Dealing with cryopreservation of
crystals grown in high salt can be a real problem, but as many people have
pointed out, the normal cryoprotectants can work, although many
I think the bash-compatible startup script has disappeared from CNS
distribution at some point. The one that was distributed with cns 1.1
still works though, and I attach my copy of it.
On 07/12/2012 11:24 AM, Dirk Kostrewa wrote:
Dear Fulvio Saccoccia,
along the lines of Ian Tickle's
Hello, Min.
Lithium sulfate is a cryoprotectant at 2.0 M and sometimes even less (much
lower than the concentrations needed for ammonium sulfate), so I would try
replacing your ammonium sulfate with lithium sulfate, creating a
cryoprotectant with 0.5-1.0 M KCl, 1.4-2.0 M LiSO4, at pH 7. You might
Hi Jan,
you will find some methods for detection of thiols and/or disulfides there:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Thiols_and_disulfides
HTH,
Guenter
Dear all,
I am working on a protein where I have to stabilize the closed
conformation of the protein using
Hi all,
We've got an old Akta prime that I think is on the verge of kicking it.
Hearing some high pitched sounds coming from the pump when we're running it.
Line A seems clogged and makes a thudding noise when we try to do a pump wash
through that line. Does anyone have any experience
Hi all,
Thanks very much to all who responded so quickly. The fix is a one liner in the
SO4.cif file (last line)
SO4 chir_01 S O1 O2 O3both
which I believe is now in the 6.3.0 release.
Interestingly the chirality parameters were not in the SO4.cif file in 6.1.3
While this change has made your symptom go away it is stretching it a bit to
call this a fix. You have not corrected the root problem that the names you
have given your atoms do not match the convention which is being applied for SO4
groups. Changing the cif means that you don't have to worry
Hi Dale,
Thanks for the input. I guess as a relatively transient user I am not
appreciating the depth of the problem. However, by at least raising this issue,
I'm hoping that the fight can be sorted out. Where does my sulfate problem
stem from? Is it from importing the fragment in COOT? Is it
Dear CCP4BBers,
just wanted to share this with you so you don't run into this issue with your
crystals.
We have 18mm 60degree angled tips and unfortunately they don't work with the
current setup at SSRL 12-2 (this is specific to this beamline and might not
apply to other microfocus lines out
Hi all,
Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org) releases
new, improved and updated versions of its tools and resources. Below is a
brief description of new features and services that have been released this
summer (or what passes as summer in the UK). As always,
Yes, it has happened to me more than once. It is not a good pump. Acta
Prime Plus has a better one. They still have parts. Call GE technical
support and they will tell you what to do.
The part costs some money (it is not cheap - probably $500). I think the
Akta Prime will keep on running as
Hi all,
Sorry for the slew of offtopic posts, but does anyone here have any experience
repacking the large 120mL Superdex75/200 columns? Any advice/tips on doing it?
I've got an older column that's gotten clogged while washing w/NaOH (can't go
over 0.1mL/min w/o getting overpressure alarm),
Hi Peter,
Most of the time it is just a clogged top filter. While the column is
running, loosen the top o-ring by loosening the black knob on the top.
Once that is done, carefully unscrew the white threaded adapter several
turns to back the top filter off the resin bed. You can then unscrew the
From: Yarrow Madrona amadr...@uci.edu
Date: July 12, 2012 7:39:57 PM PDT
To: Peter Hsu hsuu...@u.washington.edu
Subject: Re: [ccp4bb] offtopic: packing gel filtration columns
It is also likely that the clogging due to NAOH is due to crapped out
protein. Try cleaning with guanadine.
Subject: Re: [ccp4bb] offtopic: packing gel filtration columns
We do it pretty routinely in our lab with great results. To do it right you
have to invest in a reservoir sold by GE. It screws onto the end of the
column. It allows you to pour the entire slury (resin and water) into the
Hi,
Yes, it can be done by yourself. I repacked our 26/60 column a few years ago
with homemade apparatus. The column has been working for us since then.
Basically the loading apparatus was a tubing connecting the top of the
column and bottom of a reservoir (a flask with an opening near the
ad do not forget to recalibrate
On Thu, Jul 12, 2012 at 10:53 PM, Zhijie Li zhijie...@utoronto.ca wrote:
Hi,
Yes, it can be done by yourself. I repacked our 26/60 column a few years
ago with homemade apparatus. The column has been working for us since then.
Basically the loading apparatus
Sorry for the slew of offtopic posts, but does anyone here have any
experience repacking the large 120mL Superdex75/200 columns? Any
advice/tips on doing it? I've got an older column that's gotten clogged
while washing w/NaOH (can't go over 0.1mL/min w/o getting overpressure
alarm), and not
it is not cheap - probably $500
When we purchased the pump, it was below $300 (a year ago). Replacement took ~4
hours, but you must like doing it. You'll have to disassemble almost entire
pump module, so make pictures of each step and mark tubings ends with labels.
Alex
On Jul 12, 2012, at
I did not replace the entire pump, only a motor. Sorry for a confusion.
On Jul 12, 2012, at 9:28 PM, aaleshin wrote:
it is not cheap - probably $500
When we purchased the pump, it was below $300 (a year ago). Replacement took
~4 hours, but you must like doing it. You'll have to disassemble
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