On 8 Jun 2020, at 20:55, [email protected]
<mailto:[email protected]> wrote:
Re: "it turns out to be very very easy to exceed the count rate where
the detector electronics can keep up."
Sorry if this is obvious, but I take it you mean "_can't_" keep up?
Jon Cooper
On 4 Jun 2020 13:06, "Winter, Graeme (DLSLtd,RAL,LSCI)"
<[email protected] <mailto:[email protected]>> wrote:
Dear All,
A small word of caution regarding chemical crystallography on an
MX-like beamline - if you have a bright source, a well
diffracting crystal and a pixel array detector it is perfectly
possible to lose counts in the strongest reflections without
noticing - certainly without going over the nominal detector
count limits if your mosaic spread is very small
At Diamond we faced this issue with i19, which is a dedicated
chemical crystallography beamline on an undulator source, with a
Pilatus 2 detector - it turns out to be very very easy to exceed
the count rate where the detector electronics can keep up. This
is somewhat less of a problem with Pilatus 3 and Eiger 2X detectors.
So: I would strongly suggest really turning down the intensity on
the beam, use fine slicing and be prepared to check that the data
are OK before removing your sample. You can solve and refine the
structure with e.g. SHELX and get an F^2 calc vs. I ops plot
which would show systematically under measured low angle
reflections.
We also have a tool in development to bolt on to DIALS called
screen19 which estimates the true peak photon rate from a “quick
screening run” to offer insights into data collection options -
https://github.com/xia2/screen19 - this is not perfect but you
could find it useful. Our chemical crystallography users
certainly find it helpful for planning their experiments.
Best wishes Graeme
On 4 Jun 2020, at 10:51, Alker, Andre M.
<[email protected]
<mailto:[email protected]>> wrote:
Dear Jiyuan,
maybe I can add something from the small molecule
crystallographer view :-)
Crystallization:
For crystallization of small molecules you normally use
solvents and water or mixtures as mentioned already before.
At my lab the most successful way to crystallise is
evaporation. Please use small glass vials (no plastic, some
solvents will solute them too).
You can also use crystallization kits. Here you can use
Bernhard Spinglers kit and or the Hampton kit. The
Hampton kit didn't work so well for my molecules. I also
bought Bernhard's kit but had no time to test it so far. I
have to say I'm only using crystallization kits at the moment
as last try. Maybe that changes in the future.
Measurement:
Of course you can use the synchrotron for small molecules at
the protein beamline. I'm using the PXII protein beamline at
the SLS (Swiss light source) for my small molecules if the
crystals are too small for my inhouse system or there is a
problem with my inhouse system. To get the resolution you
need for structure solution and a good refinement you have to
change the wavelength to 0.7Å. Collect always at least 360
degrees in steps of 0.5 degrees or smaller. Use high filters
and short exposure times to secure your crystal against
radiation damage. Normally 10 to 20% of the beam and 0.01 to
0.1 sec work fine depending on the crystal size. Do the
measurement at low temperatures as usual for protein
crystals. Here are my parameters for the SLS-PXII beamline
equipped with an Eiger detector (wavelength 0.7Å, biggest
aperture, 20% transmission, step 0.1 deg/0.01 sec, 1800
degrees, 100K).
Processing, structure solution and refinement:
I process the eiger data with XDS,
for structure solution I'm using shelxs or shelxd,
for structure refinement shelxl.
But as mentioned before there are a lot of programs doing
processing, structure solution and refinement. I just started
to use Olex as well for solution and refinement. In very
earlier times I also used hkl2000 for data processing but in
my opinion XDS is doing a very good job for small molecule data.
Last but not least I deeply agree with Navdeep to read
Mueller et al.'s excellent book about Crystal Structure
Refinement.
Hope this helps a little bit :-)
Best regards,
André
André Alker
Senior Scientist, pCMC Analytics
Roche Pharmaceutical Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Grenzacherstrasse 124
4058 Basel, Switzerland
Phone: +41-61-6880935
email: [email protected] <mailto:[email protected]>
Upcoming absences:
...
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On Wed, Jun 3, 2020 at 7:40 PM Navdeep Sidhu
<[email protected] <mailto:[email protected]>> wrote:
Dear Jiyuan,
There was a similar question on the bulletin board some 6
years ago; my
response then (links below) complements some of the other
great
suggestions already made in answer to your question:
<https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1403&L=CCP4BB&P=R355103>,
and
<https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1403&L=CCP4BB&P=R358060>.
I believe some 90% of small molecule structures are
solved using the
SHELX suite of programs by Prof. Sheldrick, so that
should be a great
start. The programs are very easy to use, with great
defaults. (There
used to be a joke that to solve this or that problem, all
you had to do
is start one of his programs and press enter 5 times.)
As before, I'd highly recommend you read Mueller et al.'s
excellent book
with detailed tutorials. It provides the data and walks
you through
detailed examples in solving and refining small molecule
structures:
Peter Müller, Regine Herbst-Irmer, Anthony Spek, Thomas
Schneider and
Michael Sawaya. IUCr/Oxford, 2006
<http://ukcatalogue.oup.com/product/9780198570769.do>.
I'm sure you'll have much fun doing small molecules in
addition to large
molecules. We all did.
All the best,
Navdeep
---
On 01.06.20 23:50, Jiyuan Ke wrote:
> Hi Everyone,
>
> I want to crystallize a small organic molecule. I have
very limited
> experience in small molecule crystallography. I found
that the Crystal
> Screen HT from the Hampton research is good for both
small molecule and
> macromolecule crystallization. Plan to set up a sitting
drop screen just
> like setting up protein crystallization. I don’t know
if this is the
> proper way to do it. Is the MRC sitting drop 2-well
plate (HR3-083) used
> for protein crystallization good for small molecule
crystallization? Are
> there any special plates used for small molecule
crystallization? Is
> room temperature ok or not?
>
> For data collection, can I use the beamline for protein
crystals to
> collect data on small molecule crystals? Larger
oscillation angle,
> shorter exposure, reduced beam intensity?
>
> For structure determination, is SHELXL the preferred
software for
> solving small molecule structures?
>
> If anyone has experience in small molecule
crystallography, please
> help. Thanks!
>
> Best Regards,
>
> --
>
> *Jiyuan Ke, Ph.D.*
>
> *
> *
>
> Research Investigator
>
> H3 Biomedicine Inc.
>
> 300 Technology Square, Floor 5
>
> Cambridge, MA 02139
>
> Phone: 617-252-3923
>
> Email: [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>
>
> Website: www.h3biomedicine.com
<http://www.h3biomedicine.com/>
<http://www.h3biomedicine.com/>
>
>
>
>
>
>
>
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