Regarding "striking distances", there might be some shorter range effects with low energy Auger electrons but for all practical purposes I agree with James.
The main reason for this message is to ensure the original question raised by James is not forgotten as it is definitely worth resolving. Blundell and Johnson were presumably confining their remarks to room temperature. The idea of free radicals wandering around a crystal, disturbing atoms and increasing B factors over periods of hours or days does seem unlikely. However, I don't think that is necessarily what Blundell and Johnson were implying by " The chain reaction initiated by fee radical formation". I was about to put down other possibilities when I realised that these are covered in the paper by Warkentin et. al., for example in the section beginning " At temperatures above 200 K, damage arises from processes occurring on many length scales, from diffusion and reaction of radicals to solvent-coupled conformational motions to lattice-scale structural relaxations. These processes must involve an extremely broad range of timescales." The questions are 1. Whether some of the timescales are sufficiently long (at say 290K) to give observable dark progression effects with current data collection techniques (I guess James's original question) 2. Which of the processes (listed in Warkentin et. al. or other processes) is responsible for these timescales. 3. What experimental techniques do we have for studying these processes. 4. Can all this be modelled by in silico simulations (next week's job!) Colin -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James Holton Sent: 23 November 2011 19:08 To: ccp4bb Subject: Re: [ccp4bb] dark progression of radiation damage 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 > <elspeth.gar...@bioch.ox.ac.uk> 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> Jim Pflugrath >> Sent: 23 November 2011 18:11 >> To: CCP4BB@JISCMAIL.AC.UK >> 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 [CCP4BB@JISCMAIL.AC.UK] on behalf of >> Sanishvili, Ruslan [rsanishv...@anl.gov] >> Sent: Wednesday, November 23, 2011 11:49 AM >> To: CCP4BB@JISCMAIL.AC.UK >> 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 .... >> > >
