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
<[email protected]> 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:[email protected]] On Behalf Of Jim
Pflugrath
Sent: 23 November 2011 18:11
To: [email protected]
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 [[email protected]] on behalf of Sanishvili,
Ruslan [[email protected]]
Sent: Wednesday, November 23, 2011 11:49 AM
To: [email protected]
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 ....
