POST-DOCTORAL POSITION IN PROTEIN/PROTEIN INTERACTION ANALYSIS AND
PROTEIN CRYSTALLOGRAPHY, UNIVERSITY OF QUEENSLAND, BRISBANE, AUSTRALIA
Applications are invited for a post-doctoral position combining
protein/protein interaction analysis and protein crystallography, in
the laboratory of Prof
Thanks!
Phoebe
At 05:56 PM 1/22/2007, you wrote:
Hi Pheobe,
I remember an interesting paper that described how a structure revealed a
surprising role the buffer was playing in inhibition:
The 1.20 A resolution crystal structure of the aminopeptidase from
Aeromonas proteolytica complexed with
A postdoctoral position is available at the Public Health Research
Institute, New Jersey Medical School - UMDNJ, Newark, New Jersey to
perform structural and biochemical research on potential drug target
proteins from Mycobacterium tuberculosis. The candidate will be
involved in recombinant pr
Hi,
You might want to look at
Berejnov, V., Husseini, N. S., Alsaiedc, O. A. & Thorne, R. E.
(2006). J. Appl. Cryst. 39, 244-251.
Regards,
John
John Rose Ph.D.
Associate Professor
B204B, The Fred C. Davison Life Sciences Complex
120 Green Street
Department of Biochemistry and Molecular Bio
Hi,
I would suggest that you may harvest the crystals at different time, and
then mount them and test at room temperture.
Our lab has the experience that large crystals always have lower resolution
than medium size(0.1-0.2mm). So try and good luck.
deliang
- Original Message -
F
Hi Tiancen,
nobody so far has suggested to mount the smallest crystals, 0.4x0.4x0.3
seems to be pretty large, this also means that the freezing procedure is
longer. Then the other question is do you freeze in the Cryostream or by
plunging into LN2, I'd prefer the latter technique.
Good luck,
Jue
On Wednesday 24 January 2007 11:12, Daniel Anderson wrote:
> An IUCr nomenclature committee once recommended eradication of the
> "B-factor". Trueblood, et al. Acta Cryst (1996) A52, 770-781.
> Whether or not the factor of 8 pi squared can be eradicated,
> the publication is worth reading because i
page 79, chapter 5
On Wed, January 24, 2007 1:43 pm, Diana Tomchick wrote:
> Yes, it is! I somehow missed that when checking the IUCr web site.
> Virtually the whole publication is available as a series of
> downloadable PDF files, though for some strange reason the indices
> are listed but not av
Yes, it is! I somehow missed that when checking the IUCr web site.
Virtually the whole publication is available as a series of
downloadable PDF files, though for some strange reason the indices
are listed but not available. Without the Name Index it would have
taken a huge amount of time to
An IUCr nomenclature committee once recommended eradication of the
"B-factor". Trueblood, et al. Acta Cryst (1996) A52, 770-781.
Whether or not the factor of 8 pi squared can be eradicated,
the publication is worth reading because it discusses what is modeled
by Ueq (times 8 pi squared = B), and it
An interesting discussion of the development of the Debye-Waller
correction can be found in the IUCr publication, "Fifty Years of X-
Ray Diffraction," edited by P.P. Ewald (unfortunately, it's no longer
in print). It seems that Debye was the first scientist to tackle "a
problem which appeare
On Jan 24, 2007, at 11:04 AM, Bart Hazes wrote:
Carlos Frazao wrote:
Hi,
I have once heard and recently read that "the diffraction event
results from the fact that both the X-rays wavelength and the
atomic distances are of the same magnitude". Although such a
relation seems appealing I am
Hi,
I am used to have the same problem with hydrophobic ligands, in special
due to the rupture of crystals solely by the solvent even in tiny amount. So, I
decided to mix a suspension of the ligand with the crystallization drop (once
assured I can distinguish the protein from ligand). In
Tiancen,
I am not entirely clear - are you asking for techniques that can improve
your *existing* material - or are you shopping for *any* technique that
will eventually result in an improvement?
If you're looking for the latter, and are willing to send me your protein
sequence (I promise to keep
Tiancen,
One thing that you did not mention. Have you tried examining the
crystals at room temperature. Sometimes the cryo-cooling process, or
the cyro-buffer, can severely damage a crystal's long-range order. A
set of data, or just a few frames, collected at room temperature can
determine if
It looks like the earliest reference to the Debye-Waller factor is from
Debye's paper:
Uber den Einfluss der Warmebewegung uf die Interferenzerscheinungen beiu
Rontgenstrahlen, Verhandl. deut. phyik. Ges., 15, 678-689 (1913),
and the succeeding paper Verhandl. deut. phyik, Ges., 15, 738-752 (1913
Carlos Frazao wrote:
Hi,
I have once heard and recently read that "the diffraction event results
from the fact that both the X-rays wavelength and the atomic distances
are of the same magnitude". Although such a relation seems appealing I
am unsure if this is not a mere coincidence. Could some
Genentech Opportunity – Scientist, X-ray Crystallography
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I see that the [ccp4bb] has been restored to the mail Subject: line.
Thank you to the responsible party.
--
===
With the single exception of Cornell, there is not a college in the
United States where truth has ever been a welcome
For all of those that attended Study Weekend (and for those that didn't
and want to see what they missed) the photos from Study Weekend 2007 can
be found at http://www.ccp4.ac.uk/courses/stwk07/.
Hi,
Maybe a little bit off topic question but can someone remember who (as the
company) and when put the first 96 wells plate on the market?
Thanks in advance!
Andrzej
Thanks Gerard for all those explanations, I'm particularly convinced by
the last one.
Poor of me, who believed that the "B" stood for Boltzman or something
like that, I now have the correct answer!
Cheers
Virgile
Gerard DVD Kleywegt a écrit :
May be too trivial, I was just wondering
what "
Hi Carlos,
In his book "Crystals, X-rays and Proteins", Dennis Sherwood
explained in the first chapter: why do use x-rays?
Using his analogy: for a small boat (5 m length) in the ocean,
waves come in from the ocean with a wavelength (say 20 - 30 m) are
merely pass underneath the boat.
On t
On a more prosaic note, how about "bewegung?"
See Waller, I. (1927) Ann. Physik. 88:153.
Joe Becker
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Gerard DVD Kleywegt
Sent: Wednesday, January 24, 2007 10:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [c
Tricky...
My guess would be that it comes from the commonplace use of symbols in
one common definition of a Gaussian:
y = a exp( - b x^2 )
(although that doesn't explain the capitalisation).
Rajesh Kumar Singh wrote:
May be too trivial, I was just wondering
what "B" stands for in the term "B
May be too trivial, I was just wondering
what "B" stands for in the term "B-factor".
i don't really know, but i do have some wild theories, none of which are
necessarily based in fact:
- the B-factor is also called the Debye-Waller factor. now, someone assumed
that peter debye was french (in
Hi Rajesh,
I also wondered about that.
Not having been able to find a good explanation in the literature
I thought of it as reducing factor of the *B*ragg peaks. M???
Then I stopped thinking about it (I now try to call them ADPs)
Roberto
On 24 Jan 2007, at 12:42, Rajesh Kumar Singh wrote:
There's also NMP (N-methyl-2-pyrrolidone).
-- Ian
> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
> Behalf Of Green, Todd
> Sent: 22 January 2007 20:40
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [CCP4BB] crystal friendly solvents that are useful
> for dissolvin
> We have crystallized a 21KD protein with 2 disulfide bonds grown for one
> month in 0.1M tri-sodium citrate pH 5.6, 0.5M (NH4)2SO4 and 1M Li2SO4. The
> crystals look big (~0.4mm x 0.4mm x 0.3mm) and pretty (sharp edge, clean
> surface) but diffracted to only 4A in-house. The spots are quite stron
You can try DMI (1,3-dimethyl-2-imidazolidinone) as an alternative to
DMSO. Also, sometimes you get lucky, and the small molecule is more
soluble when high concentrations of glycerol are present, so you can
do the soak in a cryo buffer...
On Jan 22, 2007, at 3:40 PM, Green, Todd wrote:
H
yeah, atomic displacement parameter is abbreviated as ADP.
I wanted to know if there is some specific term
for "B" in B factor as "R" refers to Reliability in R-factor.
Rajesh
On Wednesday 24 January 2007 14:52, evrard wrote:
> Rajesh Kumar Singh wrote:
> > May be too trivial, I was just wonderin
Rajesh Kumar Singh wrote:
May be too trivial, I was just wondering
what "B" stands for in the term "B-factor".
Thanks
Rajesh
Hi Rajesh,
why, it's obvious, B stands for 'atomic displacement parameter'
Guillaume
--
**
Guillaume Evrard
European Molecular Biology La
Dear Tiancen,
for a survey of post-crystallization options, I highly recommend the following
review article:
Heras B, Martin JL. 2005
Post-crystallization treatments for improving diffraction quality of protein
crystals.
Acta Crystallogr D Biol Crystallogr. 61, 1173-80.
best of luck
Savvas
Qu
Dear Tiancen,
Try to purify your protein further by IEX column.
Sometimes it improve crystal quality drastically.
See: http://dx.doi.org/10.1107/S1744309105023080
Acta Cryst. (2005). F61, 788-790[ doi:10.1107/S1744309105023080 ]
E. Honjo, T. Tamada, Y. Maeda, T. Koshiba, Y. Matsukura, T. Okam
May be too trivial, I was just wondering
what "B" stands for in the term "B-factor".
Thanks
Rajesh
--
Rajesh Kumar Singh
Institut fur Biochemie
Universitat Greifswald
Felix-Hausdorff-Str. 4
D-17489 Greifswald
Germany
E.Mail: [EMAIL PROTECTED]
Phone: +49-3834- 86 4392
Hi,
From my rather limited experience ...
Is your EXAFS data collected on a crystal or in solution? If the
latter, it is worth remembering that the chemical environment in
solution and in crystal can be different. Moreover, atomic coordinates
and bond distances determined via crystallography a
Hi Carlos
It is more than coincidence - in that the X-rays we use for diffraction
are _chosen_ from the spectrum of X-ray wavelengths that correspond to the
interatomic distances (though this is not the only reason they are
chosen).
X-rays can be thought of as those EM waves with wavelengths from
Dear Tiancen,
I would suggest to try optimizing the hydration state of the crystal.
Either with a humidity controller (e.g. FMS system) at room temperature (or
4 degrees), with which you can optimize the diffraction,
or by partially drying the crystal on a filter paper soaked with some
precipit
As a rule of thumb from optics, you need a wavelength at least twice the
distance or shorter between two points you want to resolve. That is why we
cannot do a diffraction experiment with visible light.
On the other hand, if the wavelength were much shorter, inaccuracies in
their positions wou
Hi Carlos
Well, diffraction is a consequence of the crystal lattice repeat (or it
could be a 1-D repeat in a fibre), for without the lattice there could
be no diffraction, only scattering. But the lattice repeat is obviously
directly related to the average distance between atoms and the number of
7) Try different Cryo-protectants (can make a big difference)
8) Try to dehydrate the crystals by adding a low (5-10% w/v) concentration
of PEG20k or similar to the cryoprotectant prior to freezing
9) Anneal the crystals (a quick thaw/freeze - cover the cryostream nozzle
for ~5secs)
10) Grab the
Dear all,
Sorry for the non-CCP4 question. I think this is an old story but our knowledge
to deal with it is very limited. So any suggestions will be greatly appreciated.
We have crystallized a 21KD protein with 2 disulfide bonds grown for one month
in 0.1M tri-sodium citrate pH 5.6, 0.5M (NH4)
Hi,
I have once heard and recently read that "the diffraction event results
from the fact that both the X-rays wavelength and the atomic distances
are of the same magnitude". Although such a relation seems appealing I
am unsure if this is not a mere coincidence. Could someone clarify or
lead m
First question: do you need to run makereference at all? If you are
using a recent version, then reference data is supplied in
$CLIBD/reference_structures
In fact, if you are using the latest version of pirate, you don't need
to specify a reference structure at all.
So the only reason you mi
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