Hello All,
Sorry for this off-topic question.
I'm wondering if people could suggest an online server to identify all
kinds of hydrogen bonds and interactions in a given protein structure.
Thanks in advance.
Narayan
Order of addition when making the solutions is often important to dilute
the least soluble component rapidly. Zn acetate is the most soluble Zn
salt. Put that in your tube first and then dilute it with your largets
volume (probably either water) and then add the other ingredients, consider
vortex
While a comparison of the B factors is easy to do, interpreting its meaning
is not. The B factors are affected not only by the motion of the atoms, but
by many other factors, including the overall quality of the order of the
crystal.
The B factors for a model based on a low resolution data set
You are correct. My Friday frazzled brain is stuck in pharmacology mode so
I was thinking not of free hydroxide concentration but in terms of
potential exchangable groups being sequestered by the buffer. No more
posting on Friday. My apologies.
Katherine
On Fri, May 11, 2012 at 12:23 PM, Jacob Ke
Jacob Keller wrote:
Just to make sure I understand pH correctly: isn't it true that the
[OH-] should always be the same at a given pH (by definition)?
Maybe not by definition but by equilibration with [H+] to make water:
[H][OH]/[H2O] = Kw
[OH] = Kw[H2O]/[H]
if [W] is
It sounds as though microseeding worked very well, but the crystals are
still growing far too quickly.
Try diluting the protein and/or the reservoir solution to half the concs
you are using or lower.
To have enough protein you need larger drops, say 500 + 500 + 200 by hand
if you can't do it with
Thanks. I will try.
Rajesh
Date: Fri, 11 May 2012 12:38:20 -0500
From: j-kell...@fsm.northwestern.edu
Subject: Re: [ccp4bb] zinc with HEPES/seeding
To: CCP4BB@JISCMAIL.AC.UK
mitegen loops might help, particularly micromesh...
JPK
On Fri, May 11, 2012 at 12:35 PM, Rajesh Kumar wrote:
Dear
mitegen loops might help, particularly micromesh...
JPK
On Fri, May 11, 2012 at 12:35 PM, Rajesh Kumar wrote:
>
> Dear Patrick,
>
> You along with others had made some suggestions last time. May be its a
> good time to update.
>
> With classical screening, I got a crystal like appearances/showe
Dear Patrick,
You along with others had made some suggestions last time. May be its a good
time to update.
With classical screening, I got a crystal like appearances/shower with HEPES
7.5 and LiSo4 1.5M. Trying to vary the pH of Hepes or using Tris and with
different conc of Lithium I could o
Almost assuredly you are getting zinc hydroxide precipitate. Zn(OH)2
will readily precipitate from solutions of alkaline Zn(II). Your problem
is compounded by the fact that HEPES is a non-coordinating buffer, so it
does not help solubilize the zinc ion. You might find a weakly
coordinating buff
Just to make sure I understand pH correctly: isn't it true that the [OH-]
should always be the same at a given pH (by definition)?
JPK
On Fri, May 11, 2012 at 11:48 AM, Katherine Sippel <
katherine.sip...@gmail.com> wrote:
> That is probably because you pH Tris with HCl rather than HEPES with Na
The rationale was to see if Zn could make differences in crystal morphology.
This is because the protein has CxxC and CxxH similar to a zinc finger
motif.All my efforts, additive screening, MMS, streaking, micro batch, hanging
drop, changing drop ratio, drop shape, did not help me to either inc
That is probably because you pH Tris with HCl rather than HEPES with NaOH.
The Ksp for Zn(OH)2 is 3x10^17 so the excess hydroxides are probably what
are killing your solution.
Cheers,
Katherine
On Fri, May 11, 2012 at 11:43 AM, Rajesh Kumar wrote:
> If there is no cure , then fine.
> pH may n
pH is the culprit here
Like some already mentioned
change your pH to 6.4 and use a different buffer like cacodylate
or you can use Zinc acetate in water pH still would be 6.4
from your last mail
why would you add Zn to your initial hit condition
is there any rationale?
Padayatti
On Fri, May 11,
If there is no cure , then fine.pH may not be the answer as it doesn't Happen
with TRIS buffer pH 7.6.Thanks to every oneRajesh
Date: Fri, 11 May 2012 12:35:45 -0400
From: dj...@cornell.edu
Subject: Re: [ccp4bb] zinc with HEPES
To: CCP4BB@JISCMAIL.AC.UK
There is no cu
Initial screen was 0.1 M Hepes 7.5 and 1.25 M LiSO4. I added ZnSO4 to HEPES and
immediately it precipitated.Just now I tried to add 10 mM ZnSO4 in to tube
after volume is made up and only with HEPES 100mM pH 7.5.It happens as earlier.
So is there any way I could use Zn with HEPES. I thought ma
On 05/11/12 12:26, Rajesh Kumar wrote:
Dear All,
This question sounds simple but I dont know the answer.
I was preparing a 24 well crystal screen. When I try to use 10 mM
ZnSO4 with HEPES (pH 7.6) buffer it precipitates. I tried both ZnCl2
and Zn acetate the effect is same.
I dont know why t
Could it be that the pH is too high? Zn is amphoteric and you might be seeing a precipitate of Zn(OH)2.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Try adding water first, so that you are not mixing concentrated Zn with
concentrated HEPES. Also it depends what else is in your cocktail.
JPK
On Fri, May 11, 2012 at 11:26 AM, Rajesh Kumar wrote:
> Dear All,
>
> This question sounds simple but I dont know the answer.
> I was preparing a 24 we
Dear All,
This question sounds simple but I dont know the answer.I was preparing a 24
well crystal screen. When I try to use 10 mM ZnSO4 with HEPES (pH 7.6) buffer
it precipitates. I tried both ZnCl2 and Zn acetate the effect is same. I dont
know why this Zn in not compatible with HEPES.Could
*CASP 10: Call for targets to assess the state of the art in protein
structure modeling*
As many of you know, CASP (Critical Assessment of Structure prediction)
has been assessing the state of the art in modeling protein structure
from sequence since 1994, running a community experiment once e
I would proceed in I422 and refine to get a decent model anyway. I presume
you have one molecule in that asymmetric unit?
You don't give the pointless stats on the merging of symmetry equivalents.
That would help decide whether the I point group is the more likely. The
pseudo translation peak in P
Dear Sonali,
a friend of mine sent me some data a while ago, which also contained the
CCP4 database directories, and I was able to continue his work using my
version of CCP4. All job history, logs, results etc. appeared to be fine.
Jon
2012/5/9 sonali dhindwal
> Dear All,
>
> I want to take th
Is there a fix for this? It has been a perennial request for some time..
eleanor
On 9 May 2012 10:53, sonali dhindwal wrote:
> Dear All,
>
> I want to take the backup of all my data which i have refined using CCP4.
> Can you please guide if I copy all the ccp4 data folders and then transfer
> to
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Bishwa,
the quickest way is probably to delete the region from the PDB file
(e.g. in coot or with an editor) and run baverage again.
Cheers,
Tim
On 05/11/12 11:32, wrote:
> Hi,
>
> I would like to make the comparative study of different mutan
Hi,
I would like to make the comparative study of different mutant structures. There
is a region which is flexible and missing in some cases. Is there any direct
method of calculating the BAVERAGE of that region. I used the baverage program
in ccp4 for whole structure but would like to see the val
Hi folks
Any of you who are considering attending ECM27 in Bergen may be interested in
some of the sessions that have been arranged at this Software Fayre.
The full list of Microsymposia at ECM27 should be available in the "next couple
of days"
> From: Martin Lutz
> Date: 10 May 2012 13:48:11
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