Are the imidazole rings of the histidines distorted? If they are, it could be
water/hydroxide. If not, it is probably a cobalt ion side show.
Cheers,
Rob Meijers
EMBL Hamburg
--- On Thu, 7/7/11, Artem Evdokimov wrote:
From: Artem Evdokimov
Subject: Re: [ccp4bb] Unexplained density near cobal
Well you could have a monoclinic space group with beta = 90....0001, which
for everyone would mean 90.0 degrees. You could also have beta = exactly 90 by
pure chance. Normally the R-sym values should tell you which of the two
possibilities is the correct one.
If you obtain (an example) R-sy
Hello Everyone,
I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the
correct space group is.
The current unit cell in p212121 is 98.123 101.095 211.20190.000
90.00090.000
I fed the reflection data into Xtriage to look for twinning and
pseudotranslational NCS an
Could be a hexacoordinated cobalt with a water molecule (or a hydroxyl ion)
depending on the chemical environment...
Artem
On Thu, Jul 7, 2011 at 10:07 AM, Machius, Mischa Christian <
mach...@med.unc.edu> wrote:
> Y'all,
>
> I was wondering if anyone had any thoughts about a feature we observe w
The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is organising a scientific
symposium in Cold Spring Harbor this autumn to celebrate the 40th anniversary
of the inception of the PDB and the many scientific contributions it archives.
The meeting ("PDB40") will kick off with an evening receptio
We have a manganese binding protein that binds two Mn ions in a binuclear
complex. It turns out that one of the metal ions can move about 2.0 Å
depending on crystallization & data collection conditions (check out PDB files
1ON1 and 2F5D for the alternate conformations). In some instances we co
hey Mischa
I would guess that is a split cobalt/metal site occupancy 0.1 and 0.9 or
something like that.
If you calculate an anomalous difference map you may be able to confirm/reject
that suggestion, depending on the strength of the anomalous signal.
cheers
Preben
On 07.07.2011, at 17:07,
Postdoctoral Research Associate in X-ray and neuron protein
crystallography at Oak Ridge National Laboratory, USA
Reference Code ORNL11-93-NSSD
Eligibility Requirements
Degree: Doctoral Degree received within 60 months or currently pursuing.
Description
The main research objective of this projec
jobey,
the last two are kind of phase separation. In some cases the oil like
droplets are
more in number througout the drop.
First two are microcrystalline but the second one is
more looks like made from protein precipitate.
hope this helps
if needed please refer to Terese Bergfors website at her
There is a relatively instructive figure to what Colin describes available
from the gallery:
http://www.ruppweb.org/garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART1.htm
For B=10, at 2.5 cutoff, ripples expected; for B=100 and 2.5 A, no ripples
expected.
One can also generate w
Dear Thierry (and others)
Perhaps a bit confusing to say "a sharp feature such as an heavy atom". Heavy
atoms are, well, heavy (lots of electrons) rather than sharp. Any ripples
around them in a Fourier truncated map could swamp the lighter atoms nearby.
If Zbyszek's criteria A (and his other c
Hi Obayed,
I would start with doing some limited proteolysis with a few different
proteases followed by Mass Spec analysis of the fragments to identify
loops that are readily cut.
There is lots of info and published protocols, see e.g.
http://biowww.net/protocols/proteomics/mass_spectrometry/
I forgot to say in my email about the program AnoDe that of course it
also uses the FA values from the SHELXC output file name_fa.hkl as the
amplitudes for the 'heavy atom map' with phases (native-alpha). This
procedure is remarkably simple and effective.
George
On Thu, Jul 07, 2011 at 09:46:37A
Dear Jacob,
Andrea Thorn and I will be demonstrating such a program (called AnoDe) at
the Software Fayre at the IUCr Meeting in Madrid and it is already available
from my beta-test site on email request. AnoDe requires only two input
files: a PDB file of the refined structure and the name_fa.hkl f
14 matches
Mail list logo
