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Dear James, Thanks for pointing out this paper. Unfortunately I don't have immediate access to the full text of the paper, but a reading of the online abstract seems to raise more questions than it answers. In the example quoted their model assumes an X-ray energy of 13 keV and a flux density of 4 × 10^14 photons s-1 mm-2, but some beam-lines at 3-G sources (e.g. APS) produce an unattenuated flux density ~ 5 or 6 times this. Also at lower X-ray energies (say 8 keV) the overall absorption will be much greater (though possibly the flux density will be lower). Finally I'm puzzled by their statement "numerical analysis shows that the controlling thermal resistance is the rate of convective heat-transfer and not internal conduction". Convection of what? Isn't the crystal supposed to be completely solid @ 100K? Perhaps I should a) read the full paper before firing off questions and b) direct these questions to the authors and not to you! Cheers -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of Murray, James W > Sent: Tuesday, April 25, 2006 5:31 PM > To: [EMAIL PROTECTED]; [EMAIL PROTECTED] > Subject: RE: [ccp4bb]: Radiation damage problem > > > > Dear all, > > Modelling of the beam-heating of the crystal e.g. in A. > Mhaisekar et al J. Synchrotron Rad. (2005). 12, 318-328, > shows that unless in exceptional cases (holoferritin, > tungsten clusters at the absortion edge), beam heating is > unlikely to raise the temperature of an N2-gas cooled crystal > more than a few Kelvin, and so is unlikely to be a > significant contributing factor to radiation damage. A > primitive calculation of beam heating is available in the > RADDOSE computer program. (J. Appl. Cryst. (2004). 37, > 513-522), as well as some calculations of radiation doses. > The process of cooling a crystal from room temp to 100K is > thought to reduce radiation damage by a factor of 80 or so. > The use of Helium temperatures is known to help the problem > of specific radiation damage to metal sites in EXAFS data > collection (Proc Natl Acad Sci U S A. 2005 Aug > 23;102(34):12047-52), but the applicability to overall > crystal lifetime is less clear. > > James > > Dr. James Murray > Biochemistry Building > Department of Biological Sciences > Imperial College London > London, SW7 2AZ > Tel: +44 (0)20 7594 5276 > > > > > > -----Original Message----- > From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] > Sent: Tue 25/04/2006 17:05 > To: [EMAIL PROTECTED] > Subject: RE: [ccp4bb]: Radiation damage problem > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > In which case one might expect better stability of crystals if helium > cooling is applied (ceteris paribus). Has this been observed? > > Sebastiaan Werten. > > > ---------- > > Unless of course the crystal isn't as cold as you think it is! > Essentially all of the energy of absorbed X-ray photons must > ultimately > be degraded to thermal energy, and unless this is efficiently > conducted > to the surface where it can be removed by the cold stream, > it's going to > produce some 'hot spots' which given sufficient X-ray flux may be > sufficient to cause local melting of the water glass. There > could well > be a steep temperature gradient, liq N2 temperature at the surface and > much warmer towards the centre. Also if low molecular weight solutes > are present the melting point could be locally depressed way > below that > of pure water, so there wouldn't be quite so far to go to > cause melting. > Admittedly I haven't looked at any calculations of what order of > magnitude the heating and heat conduction effects might be > for a typical > flux and I could be way off beam but it's a least a theoretical > possibility. > > -- Ian > > > -----Original Message----- > > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > > Behalf Of James Holton > > Sent: Tuesday, April 25, 2006 3:11 PM > > To: Udupi Ramagopal > > Cc: Uhnsoo Cho; [EMAIL PROTECTED] > > Subject: Re: [ccp4bb]: Radiation damage problem > > > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > > > It is definitely true that some sensitive residues decay quite a bit > > faster than the high-resolution spots. This has been repoted > > in several > > papers now. What has not been repoted (to my knowledge) is a > > convincing > > connection between the decay of side chains involved in a crystal > > contact and the loss of high-resolution data. In all of the > > studies I > > have seen that measure the rate of loss of resolution, it is always > > tightly related to dose. If you know of a study where it has > > been shown > > to be related to something else, I would like to hear about it. > > > > I, personally, do not think that there is a connection between > > specific damage near crystal contacts and loss of resolution. My > > reasoning is that a cryo-cooled crystal is permeated by a matrix of > > glassy water. Glassy water is a SOLID. So, once cooled, > the crystal > > lattice is supported by a lot more than just crystal > > contacts. Kind of > > like an insect preserved in amber. Breaking bonds near the > > contacts are > > not going to do much more distortion to the overall lattice > > than broken > > bonds in the core or even in the solvent. Diffraction is a > > process that > > occurs over dozens of unit cells. There must be long-range > > distortions > > to impact it. Site-specific damage, formally, only impacts > > the B-factor > > of that site. > > > > -James Holton > > MAD Scientist > > > > > > Udupi Ramagopal wrote: > > > > > > > > I think some times the sensitivity of residues involved > in critical > > > cystal contacts > > > can disturb these valuable suggestions and calculations. > > > > > > Ramu > > > > > > On Mon, 24 Apr 2006, James Holton wrote: > > > > > >> *** For details on how to be removed from this list > visit the *** > > >> *** CCP4 home page http://www.ccp4.ac.uk *** > > >> > > >> > > >> > > >> Disclaimer: > > >> > > >> Radiation damage is a complex phenomenon, and many aspects > > of radiation > > >> damage at low temperature are still hard to explain, let > > alone predict. > > >> You DEFINITELY need to know things like the beamline's > > brightness and > > >> the concentrations of any atoms in your sample heavier > > than oxygen to > > >> even have a ghost of a chance of understanding the origin of your > > >> problem. > > >> > > >> However... > > >> > > >> If you are used to this beamline and you "feel" that these > > crystals are > > >> decaying faster than "normal", then the most likely > > problem is that you > > >> have a heavy atom in your sample. This will cause your > > crystal to absorb > > >> a lot more x-rays than normal (doing more damage). > > Anything heavier than > > >> oxygen is a potential problem, and stuff in the solvent > counts! The > > >> "rule of thumb" is that the "absorptivity" of an atom is roughly > > >> proportional to the atomic number. So, try doing things > > like replacing > > >> potassium with lithium or iodide with fluoride (each a > > factor of 6). > > >> Obviously, the more concentrated a heavy atom is, the > > bigger the problem > > >> will be. > > >> > > >> Since beamline brigthnesses vary by a factor of 30,000 > > from place to > > >> place, and crystal absorptivity can vary by a factor of > 10 or more, > > >> radiation damage questions can be hard to answer without > > knowing flux, > > >> beam size and sample composition. > > >> > > >> But, if you do know these things... > > >> > > >> The decay in protien crystals is generally proportional to > > absorbed dose > > >> (Joules/kg or "Gray"). Dose, in turn is proportional to fluence > > >> (photons/mm^2) and the "extinction coefficient" of your > > crystal in the > > >> x-ray range. You get fluence (photons/mm^2) from flux > > (photons/s) by > > >> dividing by the beam size to get brightness (photons/mm^2/s) and > > >> multiplying by the total exposure time (in seconds). Given > > the beamline > > >> flux, wavelength, beam size, and crystal composition the expected > > >> lifetime of your crystal can be computed with a program > > called RADDOSE > > >> (Murray et. al. JSR (2005), 12, 268-75). Or you can "google" for > > >> RADDOSE. > > >> > > >> For example, you can expect the lifetime of your crystal will be > > >> (roughly) cut in half by the addition of 4M NaCl, 5M > > NH4SO4, 1 Se per 30 > > >> residues (at 0.97A), or 150 mM CsI. > > >> > > >> -James Holton > > >> MAD Scientist > > >> > > >> > > >> Uhnsoo Cho wrote: > > >> > > >>> Dear bulletin members, > > >>> Sorry for non-CCP4 related questions. > > >>> Recently, I've got crystals which have a radiation > damage problem. > > >>> It also has a weak diffraction because of the big unit > > cell dimension > > >>> (about 300A in one direction), so I have to overexpose > > crystals even > > >>> with the synchrotron beam. > > >>> The problem is that during the data collection, the > > resolution decaded > > >>> gradually from 3 to 6A after certain number of frames > > (about 30 or 40 > > >>> frames). > > >>> Do you have any experiences or any suggestions that I can > > evade this > > >>> radiation damage? > > >>> Any suggestions will be grateful. > > >>> Thank you. > > >>> Best regards, > > >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > >>> Uhn-Soo,Cho > > >>> Graduate student in Biological Structure Department > > >>> University of Washington. > > >>> HSB G514 > > >>> 1959 NE Pacific St. > > >>> Seattle, WA 98195-7420 > > >>> Box. 357420 > > >>> Fax #206-543-1524 > > >>> Tel # 206-221-2435 > > >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > >> > > >> > > >> > > > > > > > > Disclaimer > > This communication is confidential and may contain privileged > information > intended solely for the named addressee(s). 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