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)" <graeme.win...@diamond.ac.uk> 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. <00004599f25026c0-dmarc-requ...@jiscmail.ac.uk> 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 DevelopmentRoche Innovation Center Basel
F. Hoffmann-La Roche LtdGrenzacherstrasse 1244058 Basel, SwitzerlandPhone: +41-61-6880935
Upcoming absences:...
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On Wed, Jun 3, 2020 at 7:40 PM Navdeep Sidhu <sid...@gmail.com> 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: jiyuan...@h3biomedicine.com <mailto:jiyuan...@h3biomedicine.com>
>
> Website: www.h3biomedicine.com <http://www.h3biomedicine.com/>
>
>
>
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>
>
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