Since "striking distance" is about 3 microns for the primary
photoelectron and the largest unit cell in the PDB is ~0.1 microns long,
I think that means all bets are off when trying to "connect" energy
absorbed by a heavy atom to damage somewhere else in the unit cell.
-James Holton
MAD Scientist
On 11/23/2011 10:49 AM, Jacob Keller wrote:
> I understand that absorbed dose increases with presence of heavy
> atoms, but I don't understand why that should play a role in damaging
> the crystal, as heavy atoms such as in cacodylate should probably
> usually not be near enough to protein atoms to cause problems. At
> 100K, isn't it true that secondary radiation damage plays little role
> if any? So the only problem I can think of is the case when the
> cacodylate molecule happens to be within "striking distance" of a
> protein atom when it turns into a radical (not sure what that distance
> would be). This should be relatively rare in, say, 55mM cacodylate,
> when there is only ~1 cacodylate for every 1000 waters, no?
>
> Has there been an empirical study comparing similar crystals of the
> same protein +/- solvent heavy atoms? I guess derivatives are the
> obvious example--but real derivatives always have ordered, occupied
> sites.
>
> Jacob
>
>
>
> On Wed, Nov 23, 2011 at 12:28 PM, Elspeth Garman
> <[log in to unmask]> wrote:
>> Also, cacodylate contains arsenic which is heavy, and thus has a much larger X-ray absorption cross section than do buffers constituted of lighter atoms. There is therefore a bigger dose (Joules/kg of crystal) absorbed with cacodylate in the buffer than there would be without it (and no extra diffraction strength), so that is another very good reason to avoid it, or to buffer exchange it out before the diffraction experiment.
>>
>> Elspeth
>>
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Jim Pflugrath
>> Sent: 23 November 2011 18:11
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] dark progression of radiation damage
>>
>> Any cacodylate buffer will cause gas to be produced. One only needs a minute exposure on a modern home lab source to see this happening. I suggest that everyone avoid cacodylate in their crystallization drops that end up being exposed to X-rays.
>>
>> Jim
>>
>> ________________________________________
>> From: CCP4 bulletin board [[log in to unmask]] on behalf of Sanishvili, Ruslan [[log in to unmask]]
>> Sent: Wednesday, November 23, 2011 11:49 AM
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] dark progression of radiation damage
>>
>> I think I need to clarify couple of things in my recent post about "exploding" crystals during re-mounting by a robot. First, it was a bit ....
>>
>
>
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