Almost certainly a metal ion, possibly Ni(2+) if a Ni-NTA column was used
for purification. Ni-N bond lengths are typically around 2.0 A. Additional
density is probably coordinated water molecules, which should have similar
Ni-O bond distances around 1.9 A. It is fairly common to find adventitious
I am deeply saddened to hear of Ward’s passing. He was a friend to many of us
and a tremendous supporter of structural biology. I knew him since his time at
Michigan. He championed the ways through applications of new innovations
throughout the era of synchrotron technologies and increasing
Hello, do you have any negative difference density for the current position of
the His side chain? If so, it may be in two confirmations. Just a thought.
Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com
Original Message
On 20 Jul 2020, 17:16, samer halabi wrote:
>
You could try SERp? Gave some good suggestions for our non-cristallizing
paralog. However, some of the mutants I created did not express well/were
rather insoluble. So that might be a bad idea in your case.. anyway here's the
link:
https://services.mbi.ucla.edu/SER/
Best, Matthias
Dear Herman,
The absolute configuration can be determined, although very differently
from X-ray ccrystallography.
So far, two different experimental approaches have been published:
Ma, Oleynikov, Terasaki (2017), https://doi.org/10.1038/nmat4890
and Brazda et al (2019), 10.1126/science.aaw2560
Dear Jessica,
Thank you for this positive news on electron diffraction on small molecules. A
point which is still not clear to me: is it possible to determine the absolute
configuration with electron diffraction? Some claim that it cannot be done,
others claim that it can be done using
Hi,
low expression levels could indicate (just a few thoughts):
- the protein is not folded properly and already degraded during
production which in turn may indicate problems with the construct
(insert + plasmid) itself or problems with the speed of expression (i.e.
no time to fold). Lower
Dear:
The protein was purified in 4 degree, and the expression level is low, so the
aggregation is not by high concentration; the buffer pH is 7.5 which is not
colse to the PI 8.6. It should be a dimer when function, but it was aggregated
when negative staining. Maybe I could try to add
Hi Tim,
thank you for your reply. The 1998 Schenk paper is "new" to me, I had seen this
one: https://science.sciencemag.org/content/sci/364/6441/667.full.pdf
The background of my question was about the status in practice: Is it possible
to routinely determine the absolute configuration of small
Dear Herman,
no, I don't think this is routine, yet!
First of all, instrument manufacturers need to catch up. What's on the
market is quite behind what is possible - although, I don't have the
instrument I'd love to have, but at least the meta data transfer to the
image headers only works when
Dear Shijun,
Just a reminder that the pI calculated from the sequence is not necessarily the
real pI, and sometimes can very quite a bit due to folding and oligomerization
of the protein. The first protein I ever expressed had a calculated pI of 9.2
and a real pI of 7.8 (if I remember
Thank you Tim, I had the same impression.
I am afraid that our chemists will have to wait a little longer before they
routinely can get absolute configurations from electron diffraction.
Best Herman
-Ursprüngliche Nachricht-
Von: Tim Gruene
Gesendet: Montag, 20. Juli 2020 14:21
An:
Hello,
what immediately comes into mind is phosphohistidine, especially since the
density looks rather large, but the geometry seems a bit off for that but I
cannot judge only from one angle. You could of course try to fit it in and
see how it looks.
Cheers,
Arne
On Mon, Jul 20, 2020 at 6:17 PM
Hi Herman and Tim,
Thank you Tim for a comprehensive answer! Personally, we are collecting
data using the rotation method (traditional "microED" style data
collection) and processing our data with DIALS, which cannot perform the
dynamical refinement Tim discussed. We therefore cannot determine
If there is a covalent link, maybe sending a sample off to mass spec
would be a good idea. That would remove some of the guesswork.
Dale Tronrud
On 7/20/2020 9:16 AM, samer halabi wrote:
> Hello all,
> I have few blobs in an MHC II structure I am working on, especially
> opposite to
Dear
Samer,
What king of cryo-protectant did you use ?
Such a bent density, with that size, looks like an ethylene-diol.
Best regards,
Nils Marechal
De : "samer
halabi" 30c2162795b2-dmarc-requ...@jiscmail.ac.uk
A : CCP4BB@JISCMAIL.AC.UK
Envoyé: lundi 20 Juillet 2020 18:17
Objet :
It is very saddening to hear this news. It took me a couple of days to wrap
my head around it and write.
Thank you for this obituary Bob, which captures so eloquently the breadth
of all of Ward's remarkable engagements and contributions.
I interacted with him a few times over the course of the
Hi Samer,
Did you use a His tag/Ni-NTA during purification? Sometimes Ni2+ ions leach off
the Ni-NTA - maybe the two "ears" are accompanying waters?
Ni-His co-ordination distance is pretty short
(2-2.2Å - table 3
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872550/#!po=0.69) and might
The Prehna Lab is looking to recruit an outstanding graduate student (MSc or
PhD position) to join the Department of Microbiology at the University of
Manitoba, Canada (https://home.cc.umanitoba.ca/~prehnag/).
Our lab studies how bacteria communicate with their hosts, how they communicate
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