Dear everyone:
I'm sorry for a little off-topic! I want to install HKL2000 on
ubuntu11.10 32bits, but it produces a file named info not cr_info
after run the access_prod program.And when I put info to
/usr/local/lib directory and typingHKL2000 in terminal, it display:
王瑞 wangrui...@gmail.com writes:
I'm sorry for a little off-topic! I want to install HKL2000 on
ubuntu11.10 32bits, but it produces a file named info not cr_info
after run the access_prod program.And when I put info to
/usr/local/lib directory and typingHKL2000 in terminal, it display:
Hi all -
Anybody know
a) how hazardous is cacodylate?
b) does it really matter for crystallization screens?
It seems by far the most hazardous component of the standard screens;
this 2011 paper seems to think so (bizarrely, I can't access it from
Oxford):
info is send to HKL.com to get cr_info if you have a legal version
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail:
Hi,
I guess Cacodylate is safe as long as you don't come into direct contact
with it, or dispose it off in a careless fashion. Aren't there
substances in biochemical labs which are a equally if not more harmful,
like acryamide or Ethidium Bromide, for instance?
But I agree that it should be
Hi Frank,
I worked with protein purification buffers and crystallization buffers
containing 20mM potassium cacodylate for five years or so. And yes, the
only precaution I used was gloves while weighing the chemical and while
making buffers etc. And not just me, but all of my former colleagues
Hi Frank,
As the old saying goes: it's all relative (maybe not so old actually, it's only since Einstein's relativity theory, right?). Cacodylate was used, among other things, in buffers as a substitute for phosphate, merely because it kills bugs. Nowadays, we use
azide, which is just as
Hi All,
For a tutorial, we would like to demonstrate the method of ligand
soaking in protein crystals. I am thinking about using some sort of
native ligand or inhibitor that can be easily identified in the electron
density rather than halide or heavy atom derivatization.
Does anybody have
Well originally we got these in cacodylate and not much else would diffract.
http://www.pdb.org/pdb/explore/materialsAndMethods.do?structureId=2EPH
But nowadays I have another conditions, which does not require cacodylate and
works well with Hepes.
Jürgen
On Nov 9, 2012, at 7:26 AM, Frank von
Hi Frank,
In our hands, some RNAs only crystallize out of cacodylate buffers. We would
otherwise stop using it out of health and safety concerns.
Blaine
Blaine Mooers
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young
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Dear Uli,
the geometric ligands (I3C, B3C, B4C) by Tobias Beck
(http://www.protein.ethz.ch/people/tobias/) are both commercially
available and easily identified. I3C is suitable for inhouse data
collection and provide a strong anomalous signal.
Of
Human carbonic anhydrase II and any sulfonamide. We use a variety of
alkylsulfonamides (everyone can have a different ligand and they are
easy to model) or you can use commercially available inhibitors like
benzenesulfonamide, sulfanilamide, acetazolamide, etc. A 30 second soak
is sufficient
On Fri, 2012-11-09 at 15:12 +0100, Ulrich Zander wrote:
Does anybody have a suggestion for a protein/ligand combination that
could be used for that and that is commercially available?
Perhaps lysozyme complexed with some sugar?
--
Bullseye! Excellent shot, Maurice.
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BY THE VOLKSWAGEN FOUNDATION
The recent launch of X-ray free electron lasers creates unprecedented research
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carried
Dear all, thanks for your help--I made a very simple little script using
awk, and it works excellently (anyone is welcome to it, of course). Thanks
so much for taking the time.
Jacob
On Wed, Nov 7, 2012 at 9:49 PM, Jacob Keller j-kell...@fsm.northwestern.edu
wrote:
Dear Crystallographers,
Cacodylate, being an arsenic compound, is moderately toxic. You do have
to ingest it, however, for it to be toxic. Normal lab protection should
be sufficient. It is any more concerning to me than lithium salts,
mercury, acrylamide, ethidium bromide, etc.
Having said that, we usually abandon
Dear CCP4BBers,
I have a problem in purifying protein-DNA complex for a protein that I am
interested in.
The purification of protein only has been optimized and I've get enough
yield for what I need (10 mg/2.4 L growth). And I've measured DNA binding
using Fluorescence Anisotropy. The results
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Dear Wei Huang,
if you are lucky you can form the complex as crystal in the drop (I
assume you want to crystallise the protein-DNA complex):
set up drops at high salt concentration (as low as possible to keep
the protein in solution at reasonable
Dear Wei,
If i understand your different experiment, you try to obtain your
protein DNA complex at different salt concentration with different
method to reach the final concentration.
I read that you try 150 mM KCl + 150 mM NaCl as high concentration salt,
it result in 300 mM cations and
Math may be frightening but cacodylate seems not...
With a MW of 214 for the trihydrate
a 70 kg clone needs at the 0.5 g/kg LD50 to consume about 35 g of it, which
is 0.16M.
Of a 0.1M solution you'd therefore have to drink 1.6 L or almost 4 pints.
So, prost, cheers, gsuffa, bescheid,
This sounds like a job for ammonium acetate. Use it as your salt. Purify your
complex in it and then set up drops where they wells have the amount of
ammonium acetate needed to keep your protein stable and the wells have none, or
a range of concentrations. The ammonium acetate will equilibrate
I meant where the drops have the concentration of ammonium acetate needed.
James
On Nov 9, 2012, at 10:06 AM, James Stroud wrote:
This sounds like a job for ammonium acetate. Use it as your salt. Purify your
complex in it and then set up drops where they wells have the amount of
ammonium
What program do you use for refinement?
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
I am using Refmac_5.7.0029 in CCP4ThanksSDY Date: Fri, 9 Nov 2012 20:35:48
+0200
From: mbfro...@post.tau.ac.il
Subject: Re: [ccp4bb] low-resolution and zinc
To: CCP4BB@JISCMAIL.AC.UK
What program do you use for refinement?FF
Dr Felix Frolow
Professor of Structural Biology and
Dear all
i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22
and 25 respectively..the Ramachandran plot shows 90% of the residues in the
most favorable region and with 6 residues in generously allowed and no
residues in disallowed region. But in some areas i can see density
Hi,
There has been quite a lot of discussion about this and I think
different opinions exist. I would try to keep the side chains, if
there is some evidence where they are. Otherwise I would just delete
atoms and I would not mutate them to alanine.
On Friday, 09 November 2012, Faisal Tarique wrote:
Dear all
i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22
and 25 respectively..the Ramachandran plot shows 90% of the residues in the
most favorable region and with 6 residues in generously allowed and no
residues
It is not very surprising that the affinity gets higher with lower salt, right?
Why dont you measure it under _physiological_ salt concentration? (or i assume
maybe you did?)
and of course its not as high affinity due to screening (but physiological
conditions)
of the electrostatic
On Fri, Nov 9, 2012 at 7:26 AM, Frank von Delft frank.vonde...@sgc.ox.ac.uk
wrote
Anybody know
a) how hazardous is cacodylate?
b) does it really matter for crystallization screens?
[...]
(We're being subjected to a safety review.)
I know you are in the UK but this wouldn't have
Dear Faisal,
You definitely do not mutate to alanine as that would imply for the
future user of your pdb file that it is a mutant.
Some people feel they have to keep the side chain but put the
occupancies at zero. I think this is a bad practice and strongly oppose
to it as for the future
On 11/09/12 15:43, Tommi Kajander wrote:
It is not very surprising that the affinity gets higher with lower
salt, right?
Not at all. I wanted to ask if their assay could distinguish between
specific binding and nonspecific binding, but I decided not to sidetrack
the discussion.
--
Are you trying to have Coot display the Zn-ligand bonds? That's a
different issue from having refmac recognize and use the metal-ligand
restraints in refinement. (I don't bother to have Coot do this.) Looking
at your environment distances, it looks like refmac has done a
restrained refinement,
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