of Brussels. Laboratory for Biocrystallography, led by
Prof. Sergei Strelkov, is active in structural biology and rational drug
design. The working language is English. In addition to superb facilities for
molecular biology and X-ray crystallography, there are two brand-new 200kV
cryoelecton microscopes
Dear Wu,
Just as you say there is an order of magnitude difference in intensity (one is
a sealed tube and another is a rotating anode). Our experience with MicroMax007
is that it is often possible to collect a full dataset from a medium-sized
crystal overnight. With a sealed tube, this would
Dear everyone,
In a drug discovery project where our aim is to interfere with some PPIs, we
could obtain binding of drug-like fragments in several potentially interesting
pockets on our target. We would like to make a projection on how promising
these individual pockets are. One way of doing
Moticam 5 has been working well for us for a few years now (installed on a
Leica binocular)
Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45,
d Strelkov paper cited above.
Sergei
From: CCP4 bulletin board on behalf of Sergei Strelkov
Sent: Tuesday, October 8, 2019 14:14
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coiled coil molecular replacement
Dear Tommi,
With coiled coils you cert
Dear Tommi,
With coiled coils you certainly want to use the best search model possible.
Coiled coils are elongated structures and a small local inaccuracy of your
search model may result in large differences (in terms of overall rmsd) with
respect to the true structure. Two suggestions:
1.
Dear Frank and everyone,
Thanks for useful tips. Snow in liquid nitrogen has been annoying us on a
regular basis in fact. During some synchrotron sessions, a large percentage of
crystals were covered with snow. We could never fully figure out how to get rid
of it, although filtering LN2
Dear Shengyuang,
Some further suggestions. To create a model towards MR searches, you could try
our server for modelling coiled coils:
https://pharm.kuleuven.be/apps/biocryst/ccfold.php
It takes a few seconds to run.
The reference is here: https://www.ncbi.nlm.nih.gov/pubmed/28968723
I
Dear Lumbini,
Certainly not a proof but your density looks like (di)methyl-arsinoyl-cysteine
(PDB residue type CAF). This modification can happen when the protein has been
exposed to cacodylate buffer. You can find such residues (and maps) in the PDB
entries 3LPT or 5MDI.
Best wishes,
Artem (and Beatriz),
Me bad, could have thought about that! I think you are right.
There were initially bubbles in each drop (7 in one case, 4 in the other).
At some point the bubbles exploded (it was an instantaneous process, not just
shrinking).
Kind regards,
Sergei
Prof. Sergei V.
Department of
Pharmaceutical Sciences, KU Leuven <http://pharm.kuleuven.be/anafar>
From: John R Helliwell
Sent: Friday, July 13, 2018 12:07
To: Sergei Strelkov
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Should we still keep copies of all raw data?
Dear All,
I believe this question may be of some interest.
In the past, we always stored all raw data ever collected by the lab.
With the recent advances, such as
(a) automated/on-the-fly processing offered by some (European) synchrotrons, and
(b) an ongoing discussion on centralized raw
Postdoctoral opening in structural biology (protein crystallography and drug
discovery) at KU Leuven, Belgium
There is an opening for a PhD level structural biologist (postdoc / senior
postdoc) in my laboratory
(http://pharm.kuleuven.be/Biocrystallography). KU Leuven, ranked the 35th best
We are about to recycle an old Rigaku RU-H2R rotating anode system
(Cu anode, Yale mirrors). In case anyone is interested in some parts,
please contact me as soon as possible.
Regards,
Sergei
--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Dept of Pharmaceutical and
I wanted to thank everyone who responded,
for a whole bunch of advice and suggestions!
Sergei
On 29-Jul-13 12:22 PM, Sergei Strelkov wrote:
Dear all,
In old times I, just like about any protein crystallographer,
used to work on a cluster of SGI/IRIX workstations with complete
NFS-based
Dear all,
In old times I, just like about any protein crystallographer,
used to work on a cluster of SGI/IRIX workstations with complete NFS-based
cross-mounting of hard disks.
A typical operation included:
1. A single home directory location for every user:
if my home directory was on
Dear Careina,
Could you please let us know what your cell parameters are?
And what is the twin law ('transformation') that you suspect?
Best wishes,
Sergei
Dear CCP4
I have data that is twinned with an L statistic of 0.43. It seems all
the crystals that I produced were twinned sadly. Is
Dear Tatyana,
We once had a project where the crystallization
condition contained cacodylate. The crystals diffracted
to 1.9A and survived reasonably well under the beam
(maybe there was indeed some colour change upon
exposure, I do not remember exactly).
We were working with drug soaks. The
(and it takes a lot of time for Phaser to run).
Automated approaches also did not yield a better result (as far as I can
tell). I'm convinced that the space group is C2221, but I may be wrong.
Thanks to Sergei Strelkov for the numerous useful suggestions on how to
approach the problem.
One
Dear Napoleão,
I will try to summarize our experience and give some suggestions.
Few reasons why MR with coiled coils can be very tricky, such as
their asymmetric shape and their ability to overlap onto themselves
upon a shift and rotation (for a heptad-based coiled coil, this would be a
shift
a recommendation) to Prof.
Sergei Strelkov, preferably before August 7, 2011. Applications from highly
experienced candidates with previous postdoctoral experience and excellent track
record are particularly welcome.
Selected publications:
Kuehnel K et al (2004) The VASP tetramerisation domain
April 1st, 2011
Dear Andy,
We have observed the same problem before,
and just today we could finally find an explanation.
Apparently, a new (still undocumented) functionality
was quietly introduced into few widely used oscillation data
processing programs, enabling the recording of the
Dear Dave,
Here come my five pence...
I personally found stereo graphics useful in two cases.
1. When you first introduce students to biomolecular
structure and/or biocrystallography. Showing stereo
certainly helps 'building up' the initial fascination,
which is very important of course. But
Dear Young-Tae,
The program Twister (Strelkov and Burkhard, 2002) can calculate this,
among other things. If you are interested I would gladly send you
the program.
Of course one should look into the reason for your helix having
an aberrant geometry. If it is just a slightly distorted a-helix
Dear All,
first of all, I would like to thank the many
good people who have responded to my query.
Yet another truly interesting discussion on this BB!
As a partial summary, two points:
1. Few people suggested that our high Rmerge problem
could be caused by experimental troubles
like phi angle
Dear All,
I am processing a dataset collected (not by me) with 0.1 degree
oscillations.
The diffraction is quite weak even though there is a clean diffraction
pattern to about 3A.
Either Mosflm or XDS processes the data readily with +/- default settings
but both yield a high overall Rmerge
Dear all,
Is anyone aware of a structure where the individual alpha helical
chains of a coiled coil are related by a crystallographic axis? Or does
anyone know of a coiled coil structure (dimer or higher order
oligomer) that is perfectly symmetric at least in
who have recently considered or bought
such systems could express their opinions with regard to few
points, including (1) true intensity, (2) reliability, (3) ease of service
such as alignment, filament chance, anode rebuild...
I will post a summary afterwards.
Many thanks in advance!
Sergei Strelkov
be negotiated. Please
address any further
questions and/or your application, including a
detailed CV,
publication list and a list of referees,
to Prof. Sergei Strelkov via
e-mail.
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more information.
1. A postdoctoral position is available to work with Prof. Sergei
Strelkov in
the Laboratory for Biocrystallography, Department of Pharmaceutical
Sciences,
Catholic University of Leuven. The successful candidate should have
considerable
experience in protein crystallography, especially
of a program that would convert
standard oscillation data (one-degree frames, mar225)
into such a map? What we need is a direct conversion.
There is a program in CCP4 that is able to 'visualize' the reciprocal
space, but it requires hkl's as input.
Thank you,
Sergei Strelkov
--
Prof. Sergei V
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