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CCP4BB  November 2012

CCP4BB November 2012

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Subject:

Re: vitrification vs freezing

From:

Ronald E Stenkamp <[log in to unmask]>

Reply-To:

Ronald E Stenkamp <[log in to unmask]>

Date:

Fri, 16 Nov 2012 10:26:08 -0800

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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 <[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.
>>>>>>
>>>
>
> -- 
>
>     ===============================================================
>     *                                                             *
>     * Gerard Bricogne                     [log in to unmask]  *
>     *                                                             *
>     * Global Phasing Ltd.                                         *
>     * Sheraton House, Castle Park         Tel: +44-(0)1223-353033 *
>     * Cambridge CB3 0AX, UK               Fax: +44-(0)1223-366889 *
>     *                                                             *
>     ===============================================================
>

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