Hi Javier,
You're on the exact odd nature of crystals of macromolecules, i.e. the solvent
content. Small molecule crystallographers have been FREEZING crystals in LiqN2
for data collection long before the method was introduced to macromolecular
crystallography. This works perfectly well, since there is no disordered water
in those crystals (at least in the ones I'm more familiar with, from my organic
chemistry days) and there is no need for any cryoprotectant. In crystals of
macromolecules we want to prevent the solvent from freezing and form an ice
lattice that will destroy our crystals, hence we use cryoprotectants which
cause the ice to be vitirified (maybe, in any case not to crystallize). So we
end up with a crystal of macromolecule with vitrified solvent. How we call this
entity is one thing and how we call the operation is another thing (some very
creative suggestions have been made during the thread). So while vitrified
crystal may well sound oxymoron linguistically, it may represent our true
reality as protein crystallographers. And finally, I can't resist either: how
about vitristal for what we get as the result of cryo-protection and freezing?
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Javier Gonzalez
[bio...@gmail.com]
Sent: Friday, November 16, 2012 8:35 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] vitrification vs freezing
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.
>>>
