Are these metals there in the beginning to experiment before radiation damage “destroy” them? Easy to check if X-ray fluorescence facility is installed on the beam line you are measuring. It is sensitive technique and we constantly use it in the beginning of every measurement. FF
Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 1, 2014, at 04:03 , Sanishvili, Ruslan <rsanishv...@anl.gov> wrote: >> The question about metal sensitivity to radiation cannot be answered in >> general; it needs to be discussed in specific chemical coordination >> context. > > Agreed. The author of the original question should have provided more details > about the metal in question, about the samples and the way experiment was > carried out. > >> The advice about using helical scan is horrible in this context. The >> diffraction collected by such method represents state of crystal exposed >> to constant high dose. If anything, the helical scan method is more >> suitable to study radiation damaged state of the crystal. > > I am afraid the advise was horribly misunderstood. A crystal during helical > data collection doesn't have to be exposed to constant high dose. The > exposure level is selected by the experimenter and is not intrinsic feature > of helical data collection. The advise comprised a "four-step program" and it > started by determining (in the first step) a lower dose that would still > allow making valid enzymologic (or mechanistic) conclusions. Then further > steps instructed how to lower this dose even more by using multiple crystals > (if necessary due to poor crystals quality - 2nd step), or by spreading the > same low dose over a larger volume using helical data collection - step 4. > I suspect the misunderstanding is based on a misconception that if one is > using helical data collection, one necessarily is using small beam and high > intensity, but it is not so at all. The beam size to be used is dictated by > the size of the well-diffracting volume (advised to determine in step #3). If > one has large well-diffracting volume, large beam can be used for helical > data collection as well (if the volume is larger than the beam size). > Hope it clarifies things little better. > Cheers, > N. > > > Ruslan Sanishvili (Nukri) > Macromolecular Crystallographer > GM/CA@APS > X-ray Science Division, ANL > 9700 S. Cass Ave. > Lemont, IL 60439 > > Tel: (630)252-0665 > Fax: (630)252-0667 > rsanishv...@anl.gov > > > ________________________________________ > From: zbys...@work.swmed.edu [zbys...@work.swmed.edu] > Sent: Wednesday, April 30, 2014 10:33 AM > To: Sanishvili, Ruslan > Cc: ccp4bb@jiscmail.ac.uk > Subject: Re: [ccp4bb] metals disapear > > If metal ion will be sensitive to radiation depends on its redox chemistry > and not its X-ray properties. For a metal to be affected by radiation dose > it needs to be reduced by free radicals. However, such metals are rarely > (by gene counts or deposits in PDB) present in catalytic sites of enzymes. > The most frequently occurring metal ions in catalytic sites e.g. Mg++, > Ca++, Zn++, Fe++, Mn++ lack oxidation state to which they could be reduced > by a single radical. For this reason these metals tend to be very stable > upon radiation and they are last to go. Copper is the counterexample where > radiation sensitivity is much more likely to be expected. > > Unfortunately, the original question and part of the discussion involved > generic category of metals involved in catalysis, rather then specific > one. > Magnesium is by far the the most frequently encounter metal in catalytic > sites. In redox reaction the most frequent cofactors are not metals, but > NAD or FAD. Iron is most often present in Fe-S clusters rather than as > standalone Fe++ ion. These clusters are structurally diverse and do not > necessarily participate in catalysis. If they have similar or diverse > sensitivity to radiation is not clear to me. > > The question about metal sensitivity to radiation cannot be answered in > general; it needs to be discussed in specific chemical coordination > context. > > > Separate issue: > > The advice about using helical scan is horrible in this context. The > diffraction collected by such method represents state of crystal exposed > to constant high dose. If anything, the helical scan method is more > suitable to study radiation damaged state of the crystal. > > Zbyszek Otwinowski > >> Dear Dean, >> >> You have already received excellent insight into radiation effects on >> metals. From personal experience, it doesn't take long for the metal >> occupancy to go down to 80%. Of course it is not anywhere near >> "disappearing" but then again, we don't know the details of your data >> collection and of how disappeared are your disappeared metals. >> >> I will only add that you can use modern approaches to data collection to >> minimize the adverse effects of radiation. >> >> 1. Do not chase the highest resolution and try to get what is enough to >> make your enzymologic statements valid. I.e. use less dose. >> 2. If your crystals diffract poorly, consider using several crystals to >> merge few sets of underexposed data. >> 3. For each crystal, use some sort of grid scanning (we call it rastering) >> to estimate the crystal quality. It is implemented on many beamlines >> worldwide. I will insert a shameless plug here and others can follow the >> suite... See Hilgart et al., pages 717-722 here: >> http://journals.iucr.org/s/issues/2011/05/00/issconts.html >> 4. Select the better diffracting regions of the crystal and use "vector" >> or "helical" data collection whereby your crystal is being translated >> along the specified vector as data is being collected. This feature is >> also implemented on number of beamlines, including ours (see the reference >> above). >> >> All these steps are designed for one goal - to spread the total dose over >> as much diffracting volume as possible and thus minimize the damage. >> >> Hope it helps, >> N. >> >> Ruslan Sanishvili (Nukri) >> Macromolecular Crystallographer >> GM/CA@APS >> X-ray Science Division, ANL >> 9700 S. Cass Ave. >> Lemont, IL 60439 >> >> Tel: (630)252-0665 >> Fax: (630)252-0667 >> rsanishv...@anl.gov >> >> ________________________________ >> From: CCP4 bulletin board [CCP4BB@jiscmail.ac.uk] on behalf of Dean >> Derbyshire [dean.derbysh...@medivir.com] >> Sent: Wednesday, April 30, 2014 5:33 AM >> To: CCP4BB@jiscmail.ac.uk >> Subject: [ccp4bb] metals disapear >> >> Hi all, >> Has anyone experienced catalytic metal ions disappearing during data >> collection ? >> If so, is there a way of preventing it? >> D. >> >> Dean Derbyshire >> Senior Research Scientist >> [cid:image001.jpg@01CF6470.5FA976D0] >> Box 1086 >> SE-141 22 Huddinge >> SWEDEN >> Visit: Lunastigen 7 >> Direct: +46 8 54683219 >> www.medivir.com<http://www.medivir.com> >> >> -------------------------------------------------------------------------- >> This transmission is intended for the person to whom or the entity to >> which it is addressed and may contain information that is privileged, >> confidential and exempt from disclosure under applicable law. If you are >> not the intended recipient, please be notified that any dissemination, >> distribution or copying is strictly prohibited. If you have received this >> transmission in error, please notify us immediately. >> Thank you for your cooperation. >> > > > Zbyszek Otwinowski > UT Southwestern Medical Center at Dallas > 5323 Harry Hines Blvd. > Dallas, TX 75390-8816 > Tel. 214-645-6385 > Fax. 214-645-6353 >
