if the ligand binding site is exposed to the solvent a bound ligand may help.
if the protein has is flexible domains and ligand fix it in one conformation, a
bound ligand will help even more.
All the above assuming that the purity and the concentration of the protein are
high.
George
Hi all,
we encountered an odd behaviour of REINDEX.
Snip form logfile:
Data line--- reindex HKL (h+l)/2, -k, (h-l)/2
Data line--- end
Reflections will be reindexed, and unit cell recalculated
Reindexing transformation:
(h' k' l') = ( h k l ) ( 1.0 0.0 1.0 )
We are extending the deadline because seats are still available for
RapiData 2012, the fourteenth offering of our popular course:
Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement
The course will be held 22-27 April 2012:
Yes, that is about what one would expect. I also checked a few of the
extreme outliers, and almost always can come up with a reasonable value.
Which does not remove my curiosity regarding the B_sol 70 cutoff and its
purpose.
Cheers, BR
From: Pavel Afonine [mailto:pafon...@gmail.com]
Sent:
The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron
Source (MacCHESS) has an opening for a Staff Scientist (Research Associate) to
pursue the development of novel techniques in x-ray scattering as applied to
structural biology, and to support users at MacCHESS. There
Once upon a time, it was customary to apply a 3-sigma cutoff to each and
every spot observation, and I believe this was the era when the "~35%
Rmerge in the outermost bin" rule was conceived, alongside the "80%
completeness" rule. Together, these actually do make a " reasonable"
two-pronged cr
Frank,
Don't you already get a plot of SigmaA versus resolution from refmac,
where the free set of reflections has been used to estimate SigmaA?
Have a look at some of your log files.
Pete
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fra
Hi Bernhard,
I just calculated k_sol and B_sol for all PDB entries that
- have reflection data available,
- I could re-compute the R-factor within 5%, and
- R-work<30%
using a simple cctbx script. Here is what I get:
Distribution of k_sol:
0.000 - 0.060 : 27
0.060 -
Dear All,
when I plot bulk solvent B and K extracted from EDS, an improbable and
bimodal distribution appears.
In the B_sol vs k_sol PDF a sharp line of values with B-sol of 70 appears
(B-axis left to right, 0-200).
http://www.ruppweb.org/images/b_sol_contour.jpg
http://www.ruppweb.org/images/b_
On Jan 30, 2012, at 10:28 AM, Jacob Keller wrote:
>> I'm intrigued: how come this apparently excellent idea has not become
>> standard best practice in the 14 years since it was published?
>
> It would seem because too few people know about it, and it is not
> implemented in any software in the
> I'm intrigued: how come this apparently excellent idea has not become
> standard best practice in the 14 years since it was published?
It would seem because too few people know about it, and it is not
implemented in any software in the usual pipeline. Maybe it could be?
Perhaps the way to do i
Dear Christian
When I run this data into Pointless it doesn't find any higher symmetry than
I422. However, the data appear to be highly twinned so I would be wary of
believing that.
If you put a merged file into Pointless, it can check for under-merging, but
you can't really expect to use the
Somebody sent this to me after a previous post a while back--a sort of
case-study:
Wang, J. (2010). Inclusion of weak high-resolution X-ray data for
improvement of a group II intron structure. Acta crystallographica
Section D, Biological crystallography 66, 988-1000.
JPK
On Mon, Jan 30, 2012
Pointless can really only determine the space group from an unmerged file which
wouldn't contain a merged amplitude F, so I'm not quite sure what you are
trying to do
Can you send me the file & your command off-list & I'll check
best wishes
Phil
On 30 Jan 2012, at 13:54, Christian Roth wrote:
Hi,
I want determine the spacegroup with pointless and it should directly write
out the mtz in the best sg. When I give a mtz with Structure Factor amplitude
pointless recognize the file (9 columns) change the space group and the new
file
in the new space group has just 7 columns and FP and S
Does your kinase autophosphorylate by any chance? -- That can produce
differently phosphorylated species and affect crystallisability. You can
detect it by e.g. mass spec, and tackle it by dephosphorylating the
protein prior to crystallisation or by coexpression with a phosphatase.
From: CCP
Staurosporine come to mind as a general kinase inhibitor. I also second
Artem's suggestion that ligands make a big difference, we had several
cases of kinases which required ligands for crystallization success.
Also make sure you eliminate any floppy ends which may interfere with
packing.
Good
It is a fairly common issue with kinases. Among other options you may want
to try a generic kinase inhibitor (there are several good ones just look at
pdb structures for ieas) and if this does not help then you could attempt
to clamp the motion down via an inter-lobe engineered disulphide bond...
---
Postdoctoral position in DNA Damage Response Group at the Paterson Institute
for Cancer Research, Manchester
-
Do remember you can assign chirality as both.. This can be useful as
otherwise the refinement programs force the requested chirality and
espec at low resolution it can be hard to see any indication of error..
..
Eleanor
On 01/27/2012 09:06 AM, herman.schreu...@sanofi.com wrote:
Dear Debajyoti
ESPript is a good option too: http://espript.ibcp.fr/ESPript/ESPript/
Good luck,
Jon
2012/1/30 Florian Brückner
> Hi Sreetama,
>
> you can use STRAP for that: http://3d-alignment.eu/. It allows you to do
> multible sequence alignments and use various algorithms to predict
> secondary structure
Hi Sreetama,
you can use STRAP for that: http://3d-alignment.eu/. It allows you to do
multible sequence alignments and use various algorithms to predict secondary
structure or display secondary structure assignments of PDB entries.
Cheers
Florian
Am 30.01.2012 um 11:02 schrieb sreetama das:
Dear all,
I am trying to crystallize a protein kinase without any success.
I suspect about its characteristic catalytic loop. I have already prepared
different constructs, different expression vectors, and different mutant
proteins (pseudo-phosphorylated, active, inactive?). I have also tes
Hi Randy - thank you for a very interesting reminder to old literature.
I'm intrigued: how come this apparently excellent idea has not become
standard best practice in the 14 years since it was published?
phx
On 30/01/2012 09:40, Randy Read wrote:
Hi,
Here are a couple of links on the ide
Dear All,
Is there any module in CCP4/ other related software/servers which
can show a multiple alignment of homologous sequences from a protein family,
together with their secondary structures?
Thanks in advance,
regards,
sreetama
Hi,
Here are a couple of links on the idea of judging resolution by a type of
cross-validation with data not used in refinement:
Ling et al, 1998: http://pubs.acs.org/doi/full/10.1021/bi971806n
Brunger et al, 2008:
http://journals.iucr.org/d/issues/2009/02/00/ba5131/index.html
(cites earlier
Postdoctoral Position and PhD positions in Structural Biology
at the Max Planck Institute for Medical Research, Heidelberg.
The Meinhart lab in the Department
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