Hi Giorgio,
some XDS-related hints can be found at
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Small_molecules
which I renamed to "Difficult datasets" since some of the suggestions also
apply to those.
What is lacking in that article is that you really should specify
SENSOR_THI
Hi,
- If ur protein is making strong complex then You can run Native
page with increasing concentration of your inhibitor peptide
and decrease in complex band intensity will show you competitive binding of
your inhibitor to proteins.
- You can do ELISA... by coating one of
Hi Garib,
Thanks for that (and thanks Herman). How do I declare a non-natural amino acid
a peptide? My ligand contains two peptidic cycles (non-N to C) where the side
chains are cyclised. I think I'll be able to use several linbk records for the
connections but the non-natural amino acid are co
Dear CCP4ers,
I'd purchased a stereo monitor from Sharper Technology with a Planar SA2311W
stereo 3D LCD and the Nvidia 3D vision kit. However, I'm having a problem
with the dual monitor setup. Everything works fine with Pymol and Coot when
using a single 3D capable monitor (Planar SA2311W) and N
Most beamlines have attenuators, so there's little reason to collect
multiple sweeps. We always collect 360deg. Since it's a small molecule,
and usually fairly large and robust, you can warm it up, nudge it in a
different direction with a pin (we use sterile, disposable acupunture
needle), and refr
Giorgo,
We have done that routinely for quite some time now. We had problems
when using a normal CCD detector, where we had to collect two or three
sweeps to avoid overloads (see below). Since we have the PILATUS this is
not necessary anymore and the data behaves fine. "Problems" still
persisting
Pius,
The situation you describe is an off-equilibrium situation. You have
applied a perturbation
and that may not be reversible!
Enrico.
On Wed, 08 Feb 2012 16:35:56 +0100, Pius Padayatti
wrote:
Hi Enricho,
The scenario of streak seeding follows Ostwald ripening but will
this happen
On 02/08/12 12:47, Clemens Vonrhein wrote:
On Wed, Feb 08, 2012 at 12:45:35PM -0500, David Schuller wrote:
It worked just as you said, but I don't read Japanese so it wasn't
particularly helpful.
Odd ... at
http://web.archive.org/web/20080927013137/http://idb.exst.jaxa.jp/db_data/protein/s
It worked just as you said, but I don't read Japanese so it wasn't
particularly helpful.
Thanks.
On 02/08/12 11:37, Clemens Vonrhein wrote:
Hi,
the "waybackmachine" at
http://www.archive.org/
helps here. Just type
http://idb.exst.jaxa.jp/
into the box and hit "Take me back". It then
Hello everybody,
This is slightly off-topic but I still hope there might be somebody in the
crowd with (Py)Rosetta experience. I successfully tried protein_protein
docking before, but now I am trying to dock a RNA into a protein using
PyRosetta v.1.1, which, as you can imagine, fails in a new an u
Dear All,
The Ho lab at the Institute of Biological Chemistry of Academia Sinca in Taiwan
seeks to recruit a motivated structural biologist at post-doctoral level with
interest in structure and activity studies of pharmaceutically important
enzymes.
Applicant should have a strong background in
Hi Giorgio, there are beamlines dedicated to small molecule crystallography at
synchrotrons as well. I can suggest I19 at Diamond (obviously) but there are
others!
http://www.diamond.ac.uk/Home/Beamlines/I19.html
Martin
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCM
I collected GTP/Mg2+ crystal on SSRL beamline 9-1 before. The images
was processed by Mosflm and structure was solved by Shelx as usual.
Kevin
On Wed, Feb 8, 2012 at 3:41 AM, Giorgio Giardina
wrote:
> Hello,
> I have some interesting small molecule xtals.
> I was wondering if it is possible to
Hi Enricho,
The scenario of streak seeding follows Ostwald ripening but will
this happen in other situations as follows
But in a special case where you have some crystals that appear as large
rods which dissolved when taken out of the incubator (or) during the
observation( these were antibody-comp
On 02/08/12 06:49, Enrico Stura wrote:
On Wed, 08 Feb 2012 12:08:23 +0100, Theresa H. Hsu
wrote:
A little off from the original question. Why don't small crystals
dissolve to make a bigger crystal, especially when the small ones
grow on top of each other?
Sometimes they do. Key phrase
Roger Rowlett wrote:
No. Kw = [H3O+][OH-] = 1 x 10^-14 at 25 deg C.
So at pH 7.0, you have 10^-7 M each at equilibrium no matter how you slice it
or whatever
else is in solution. If equilibrium [H3O+] goes up [OH-] goes down
commensurately.
The "pKa" of water as an acid is based on Kw and wat
Hello Jiahong:
If I understand correctly that you want to test protein-protein interaction or
inhibition study in solution, maybe you can try something like ELISA to test
protein-protein interaction. Or if your B protein has 6 histag, you can use
Ni-NTA agrose beads to test inhibition or bindi
I notice links in various places to "JAXA Cryoprotectant Database for
protein crystals"
http://idb.exst.jaxa.jp/db_data/protein/200304E02478000.html
But when I follow the links, I get:
"Forbidden - You dont have permission to access..."
Is this data base still available? Is there another good s
Jiahong
Thermo sells a series of kits called DyLight Fluor for fluorescent
labelling of antibodies or other proteins. They have everything you need
and they're very convenient and easy to use. You can pick the excitation
and emission wavelength. If you label both A and B (or C) with different
"
Dear all,
I am looking for some kind of dye for protein affinity comparison, but do not
know which to choose.
I know protein A can contact B to form a complex,now I hope to find something
simiar with A to act as an inhibitor to block the process of A-B complex
formation. Maybe a short peptide
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello Giorgio,
most synchrotron beamlines should have a resolution limit beyond or near
1A resolution which is sufficient for solving the structure with direct
methods.
At least XDS has no problems with non-chiral space groups and can be
used to proc
Hello,
I have some interesting small molecule xtals.
I was wondering if it is possible to collect a small molecule data-set using a
sincrotron macromolecular xtallography beam line, maybe with a very low beam
intensity and moving the detector as close as possible?
Has anybody experienced that?
A
Theresa,
A little off from the original question.
You should have started a new thread.
The answer to your question is very simple. Small crystals will dissolve
when the degree of saturation
of the solution becomes too low to support their relatively high surface
to volume ratio.
The larg
A little off from the original question. Why don't small crystals dissolve to
make a bigger crystal, especially when the small ones grow on top of each
other? Can the clustered 3D crystals (I think it is called macroscopic twin) be
used for full data collection?
Again, thank you.
Theresa
Hi Joel
Herman is right:
If you are refining cyclic peptides then the easiest way is to use link record
linking C-terminus with N terminus. the name of the link should be TRANS. Here
is an example:
LINK ALA S 21 ASN S 1TRANS
It will force ALA
Hi Joel,
The way I solved this problem was by generating a linear peptide and
then connecting the ends using a LINK card in the header of the pdb.
Good luck!
Herman
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Joel Tyndall
If you find yourself in the situation where the buffer you started with is out
of range of the pH you would
like to attain, there are sets of buffers you can use that contain most of the
standard buffers that will give
you a fairly linear response across ~4-10, as described by Newman, Acta Crys
Dear all,
Is there any program that can view the fragment files generated from
Rosetta Fragment library?
For example, I want to build a model myself, and I know the secondary
structure of the target protein, so I will dock the 9-fragment myself.
But, at the first step, I have to choose one fragm
Hello Sreetama:
I think for crystallization, everything is hard to say. But if you find your
crystal is sensitive to the pH, you certainly can optimize the pH value but it
is better not to deviate a lot. For example you can make 0.2 unit interval (for
example: pH value 4.5, 4.7, 4.9...etc which
Dear Nick,
If you're happy to keep on using xia2, you can just put both of the
data sets in a single directory and run
xia2 -3dii /heres/where/the/data/went
And wait a little while.
To comment on your analysis of the statistics: inside xia2 the scaling
is switched off as far as possible in the
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