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 <[log in to unmask]>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.
> > >>>
> >
--
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