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:[EMAIL PROTECTED] On Behalf Of Ian Tickle Sent: 06 May 2008 11:26 To: [email protected] 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: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Lijun Liu > Sent: 05 May 2008 21:37 > To: James Holton > Cc: [email protected] > 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 > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674 <DIV><FONT size="1" color="gray">This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom </FONT></DIV>
