Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line
Hi Giorgo, Just to say that we routinely, and often, do these sorts of experiments on ID29 and ID23-1 at the ESRF using an energy of 20 keV (~0.62 Angstrom wavelength) and detector distances that allow collection of data to a resolution of better than 0.7A. Mini-kappa goniometers also allow for the collection of data in more than one crystal orientation in the case of completeness problems. As has already been pointed out by others who have replied to your posting, the processing of the images with MOSFLM or XDS is usually pretty straightforward as is structure solution using direct methods. Hope this helps Gordon At 12:41 08/02/2012, Giorgio Giardina wrote: 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? And if I get the images back home, can I process them using standard macromolecular software or do I need ab-initio special programs? Will MR work for phasing? Thanks in advance, Giorgio
Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line
You have been all wonderfully helpful. The landscape is crystal-clear now. Thanks to everybody. Giorgio
[ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line
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? And if I get the images back home, can I process them using standard macromolecular software or do I need ab-initio special programs? Will MR work for phasing? Thanks in advance, Giorgio
Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line
-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 process the data. Since with a small cell you are going to have only few spots per image, make sure you increase the DELPHI parameter to 30 or 60, as Kay Diederichs pointed out to me. XDS_ASCII.HKL can be read into xprep which, if you keep on hitting enter and provide it with the chemical composition when it asks you to, is going to prepare a shelxd input file that can be used to solving the structure with shelxd. Its output .res-file is the starting point for refining the structure with e.g. shelxl. So: yes, you can process the data with [sparkle ;-)] standard macromolecular software [/sparkle] Cheers, Tim On 02/08/2012 12:41 PM, Giorgio Giardina wrote: 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? And if I get the images back home, can I process them using standard macromolecular software or do I need ab-initio special programs? Will MR work for phasing? Thanks in advance, Giorgio - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPMmgSUxlJ7aRr7hoRAtb7AKDhMgf+ImXfp/qR4WwR/AhCM1Wj6ACgh93K jpXsZgiGY9CfBHmMHd+L928= =dW6B -END PGP SIGNATURE-
Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line
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 giorgio.giard...@uniroma1.it wrote: 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? And if I get the images back home,  can I process them using standard macromolecular software or do I need ab-initio special programs? Will MR work for phasing? Thanks in advance, Giorgio
Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line
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@JISCMAIL.AC.UK] On Behalf Of Giorgio Giardina Sent: 08 February 2012 11:42 To: ccp4bb Subject: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line 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? And if I get the images back home, can I process them using standard macromolecular software or do I need ab-initio special programs? Will MR work for phasing? Thanks in advance, Giorgio
Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line
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 are: we have only a single axis goniometer, which can lead to low completeness in P1 and P-1. Highest energy (17keV) and closest distance (188mm) at our beamline have many SM crystals (even the ones that don't diffract in house -- that is a 300 or 500 u sealed tube) with an I/sig of 5-10 at the edge of the detector. Crunch, Acorn, ShelxCDE and ShelxS don't have any problem with any of the data we collected to 0.9A resolution. The multipass caused some inexplicable non definite positives during refinement. We haven't tracked that down systematically, so it might just have happened haphazardly. HTH, Jens On Wed, 2012-02-08 at 11:41 +, Giorgio Giardina wrote: 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? And if I get the images back home, can I process them using standard macromolecular software or do I need ab-initio special programs? Will MR work for phasing? Thanks in advance, Giorgio
Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line
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 refreeze it in the cryostream. Then do a second sweep in a different orientation. I recommend moving the beam energy to 15.5KeV or higher to compress the diffraction image. Collect with 5-10deg widths. We can typically get the detector to around 70-80mm. You need to get to 0.85A resolution or better for good, stable refinement, and Acta Cryst. requires that resolution for publication. Often you need the low-resolution data and data to better than 1A to help with the sigma2 relationships in direct methods. You see both primary and secondary extinction, and that extinction can be anisotropic, so the SWAT option in SHELX is most useful. Otherwise, the overall scale factor is off, typically overestimated by the strong low-resolution reflection intensities, with the result that the anisotropic Gaussian displacement parameters may become non-positive definate. Bernie On Wed, February 8, 2012 12:46 pm, Jens Kaiser wrote: 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 are: we have only a single axis goniometer, which can lead to low completeness in P1 and P-1. Highest energy (17keV) and closest distance (188mm) at our beamline have many SM crystals (even the ones that don't diffract in house -- that is a 300 or 500 u sealed tube) with an I/sig of 5-10 at the edge of the detector. Crunch, Acorn, ShelxCDE and ShelxS don't have any problem with any of the data we collected to 0.9A resolution. The multipass caused some inexplicable non definite positives during refinement. We haven't tracked that down systematically, so it might just have happened haphazardly. HTH, Jens On Wed, 2012-02-08 at 11:41 +, Giorgio Giardina wrote: 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? And if I get the images back home, can I process them using standard macromolecular software or do I need ab-initio special programs? Will MR work for phasing? Thanks in advance, Giorgio -- Bernard D. Santarsiero Research Professor Center for Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy Center for Structural Biology Center for Clinical and Translational Science University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds
Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line
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_THICKNESS= and SILICON= . This is already taken care of in the Pilatus XDS.INP templates, but for CCD detectors this has to be specified manually; see hints in the script http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP HTH, Kay
