I was going to mention that too, but since I was a postdoc of Petsko my words could have been viewed as biased.
Quyen On Nov 16, 2012, at 1:26 PM, Ronald E Stenkamp <stenk...@u.washington.edu> wrote: > I'm a little confused. Petsko and others were doing > low-temperature/freezing/vitrification crystal experiments in the 1970s, > right? (J. Mol. Biol., 96(3) 381, 1975). Is there a big difference between > what they were doing and what's done now. > > Ron > > On Fri, 16 Nov 2012, Gerard Bricogne wrote: > >> Dear all, >> >> I think we are perhaps being a little bit insular, or blinkered, in >> this discussion. The breakthrough we are talking about, and don't know how >> to call, first occurred not in crystallography but in electron microscopy, >> in the hands of Jacques Dubochet at EMBL Heidelberg in the early 1980s (see >> for instance http://www.unil.ch/dee/page53292.html). It made possible the >> direct imaging of molecules in "vitrified" or "vitreous" ice and to achieve >> higher resolution than the previous technique of negative staining. In that >> context it is obvious that the vitreous state refers to water, not to the >> macromolecular species embedded in it: the risk of a potential oxymoron in >> the crystallographic case arises from trying to choose a single adjective to >> qualify a two-component sample in which those components behave differently >> under sudden cooling. >> >> I have always found that an expression like "flash-frozen" has a lot >> going for it: it means that the sample was cooled very quickly, so it >> describes a process rather than a final state. The fact that this final >> state preserves the crystalline arrangement of the macromolecule(s), but >> causes the solvent to go into a vitreous phase, is just part of what every >> competent reviewer of a crystallographic paper should know, and that ought >> to avoid the kind of arguments that started this thread. >> >> >> With best wishes, >> >> Gerard. >> >> -- >> On Thu, Nov 15, 2012 at 11:35:46PM -0700, Javier Gonzalez wrote: >>> Hi Sebastiano, >>> >>> I think the term "vitrified crystal" could be understood as a very nice >>> oxymoron (http://www.oxymoronlist.com/), but it is essentially >>> self-contradictory and not technically correct. >>> >>> As Ethan said, "vitrify" means "turn into glass". Now, a glass state is a >>> disordered solid state by definition, then it can't be a crystal. A >>> vitrified crystal would be a crystal which has lost all three-dimensional >>> ordering, pretty much like the material one gets when using the wrong >>> "cryo-protectant". >>> >>> What one usually does is to soak the crystal in a "cryo-protectant" and >>> then flash-freeze the resulting material, hoping that the crystal structure >>> will be preserved, while the rest remains disordered in a solid state >>> (vitrified), so that it won't produce a diffraction pattern by itself, and >>> will hold the crystal in a fixed position (very convenient for data >>> collection). >>> >>> Moreover, I would say that clarifying a material is vitrified when >>> subjected to liquid N2 temperatures would be required only if you were >>> working with some liquid solvent which might remain in the liquid phase at >>> that temperature, instead of the usual solid disordered state, but this is >>> never the case with protein crystals. >>> >>> So, I vote for "frozen crystal".- >>> >>> Javier >>> >>> >>> PS: that comment by James Stroud "I forgot to mention that if any >>> dictionary is an authority on the very cold, it would be the Penguin >>> dictionary.", is hilarious, we need a "Like" button in the CCP4bb list! >>> >>> -- >>> Javier M. Gonzalez >>> Protein Crystallography Station >>> Bioscience Division >>> Los Alamos National Laboratory >>> TA-43, Building 1, Room 172-G >>> Mailstop M888 >>> Phone: (505) 667-9376 >>> >>> >>> On Thu, Nov 15, 2012 at 2:24 PM, Craig Bingman >>> <cbing...@biochem.wisc.edu>wrote: >>> >>>> "cryopreserved" >>>> >>>> It says that the crystals were transferred to cryogenic temperatures in an >>>> attempt to increase their lifetime in the beam, and avoids all of the other >>>> problems with all of the other language described. >>>> >>>> I was really trying to stay out of this, because I understand what >>>> everyone means with all of their other word choices. >>>> >>>> On Nov 15, 2012, at 2:07 PM, James Stroud wrote: >>>> >>>>> Isn't "cryo-cooled" redundant? >>>>> >>>>> James >>>>> >>>>> On Nov 15, 2012, at 11:34 AM, Phil Jeffrey wrote: >>>>> >>>>>> Perhaps it's an artisan organic locavore fruit cake. >>>>>> >>>>>> Either way, your *crystal* is not vitrified. The solvent in your >>>> crystal might be glassy but your protein better still hold crystalline >>>> order (cf. ice) or you've wasted your time. >>>>>> >>>>>> Ergo, "cryo-cooled" is the description to use. >>>>>> >>>>>> Phil Jeffrey >>>>>> Princeton >>>>>> >>>>>> On 11/15/12 1:14 PM, Nukri Sanishvili wrote: >>>>>>> s: An alternative way to avoid the argument and discussion all together >>>>>>> is to use "cryo-cooled". >>>>>>> Tim: You go to a restaurant, spend all that time and money and order a >>>>>>> fruitcake? >>>>>>> Cheers, >>>>>>> N. >>>>>>> >>>> >> >> -- >> >> =============================================================== >> * * >> * Gerard Bricogne g...@globalphasing.com * >> * * >> * Global Phasing Ltd. * >> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * >> * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * >> * * >> =============================================================== >>
