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Hi
Just for completeness (seeing as we are discussing scattering factors
and radiation damage) there is an increased susceptibility to primary
damage for sulphur due to the increased absorption which follows f'',
tabulated for example in
http://henke.lbl.gov/optical_constants/asf.html. The x-ray absorption of
the sample is related to these.
f'' for nitrogen is 0.034 at 6keV and 0.007 12keV
f'' for sulphur is 0.936 at 6keV and 0.258 12keV
Much greater absorption for sulphur and much more likely to be damaged
by direct absorption of a photon.
However this direct primary damage is not the main factor. Each absorbed
photon produces a high energy photoelectron (ejected from the absorbing
atom). This photoelectron gradually loses energy as it travels through
the sample, creating several hundred sites of secondary damage. These
damaged sites are the main effect, rather divorced from the initial
absorption site. Weak bonds are more likely to be disrupted due to these
inelastic interactions with the photo-electron. Even then, one will not
see an effect (by x-ray diffraction) unless the atom has some freedom
(at approx 100K) to move within its local environment. This is more
likely to happen on the outside of the protein rather than in the
interior.
Cheers
Colin
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Ian Tickle
Sent: 06 May 2008 11:26
To: [log in to unmask]
Subject: Re: [ccp4bb] Negative density around C of COO-
Hi, I think you'll find that if you work out the contribution from f' to
the density, in most cases it's not significant relative to the RMSD.
This will be particularly true for S which of course has a low value of
f' for all commonly used wavelengths. This must be true otherwise we
would observe these effects routinely. The explanation must involve
some effect which is peculiar to the crystal being studied, as opposed
to being peculiar to the wavelength, and radiation damage seems the most
likely explanation (and has been unequivocally demonstrated in a number
of cases).
-- Ian
> -----Original Message-----
> From: [log in to unmask]
> [mailto:[log in to unmask]] On Behalf Of Lijun Liu
> Sent: 05 May 2008 21:37
> To: James Holton
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] Negative density around C of COO-
>
> I believe some, may not be all, negative density may be due to the
> choice of wavelength. C,O and N are not so sensitive to normally used
> wavelength (1-1.54A), but S does. This is more true when you have
> higher resolution and better quality data. You can estimate this by
> f'.
>
> By the way, although I am not a real supporter of "radicals from
> damage", I believe that a photo-induced (here X-ray) chemical reaction
> is much different from a heat-induced one.
> Low temperature is not a problem. But this not for diffusion, as it
> is ~100% heat-related. Please point out if I am wrong.
>
> This "assignment" of free radicals to damage is often made
> (flippantly) in the literature, but I feel a strong need to point out
> that there is NO EVIDENCE of a free radical diffusion mechanism for
> radiation damage below ~130K.
>
>
> Lijun Liu, PhD
> Institute of Molecular Biology
> HHMI & Department of Physics
> University of Oregon
> Eugene, OR 97403
> 541-346-4080
>
>
>
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