[ccp4bb] 回复： [ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure
Dear Tanya, We have published a paper related to this topics on PloS One last year (see below), and we have not generally encountered "crystal degradation pattern upon X-ray exposure". "Get phases from arsenic anomalous scattering: de novo SAD phasing of two protein structures crystallized in cacodylate buffer." Liu X, Zhang H, Wang XJ, Li LF, Su XD. PLoS One. 2011;6(9):e24227. Epub 2011 Sep 2. Xiao-Dong Su, Professor Chairman of the Commission on Biological Macromolecules (CBM), International Union of Crystallography (IUCr); Secretary-general, Chinese Crystallographic Society(CCrS); School of Life Sciences, Peking University 100871 Beijing, China Phone: +86-10-62759743 FAX: +86-10-62765669 E-mail: x...@pku.edu.cn - 原始邮件 - 发件人: Tatyana Sysoeva 收件人: CCP4BB@JISCMAIL.AC.UK 已发送邮件: Mon, 30 Jul 2012 06:53:13 +0800 (CST) 主题: [ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure Hi! I heard a couple of times that use of cacodylate buffers in crystallization is bad, and not only because of the compound toxicity. As I understood, presence of the cacodylate in a protein crystal will cause a particular crystal degradation pattern upon X-ray exposure - "darkening of the crystals, gas formation" I tried to find some references on that and failed in doing so. I found some earlier discussions like this one: http://www.proteincrystallography.org/ccp4bb/message23691.html but don't have anything to reference in literature. I would appreciate if someone can point me to a right direction. I am sorry if this question is out of the groups topic range. Thank you in advance! Sincerely, Tanya
Re: [ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure
Hi Tanya - did you read the next message in the thread you posted? It answers the question, even if somewhat succinctly: http://www.proteincrystallography.org/ccp4bb/message23692.html The April 2011 issue of Journal of Synchrotron Radiation has the proceedings from the 2010 Radiation Damage workshop; those papers and their references are an excellent starting point if you want to know more of the gory details. Cheers phx On 02/08/2012 23:50, David Schuller wrote: I do not have the reference you are seeking, but I have seen cacodylate-containing xtals diffract to better than 1.2 and hold up very well. Also, arsenic has an anomalous signal which may be exploited for phasing, peak ~ 1.04 A. On 07/29/12 18:53, Tatyana Sysoeva wrote: Hi! I heard a couple of times that use of cacodylate buffers in crystallization is bad, and not only because of the compound toxicity. As I understood, presence of the cacodylate in a protein crystal will cause a particular crystal degradation pattern upon X-ray exposure - "darkening of the crystals, gas formation" I tried to find some references on that and failed in doing so. I found some earlier discussions like this one: http://www.proteincrystallography.org/ccp4bb/message23691.html but don't have anything to reference in literature. I would appreciate if someone can point me to a right direction. I am sorry if this question is out of the groups topic range. Thank you in advance! Sincerely, Tanya -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure
I do not have the reference you are seeking, but I have seen cacodylate-containing xtals diffract to better than 1.2 and hold up very well. Also, arsenic has an anomalous signal which may be exploited for phasing, peak ~ 1.04 A. On 07/29/12 18:53, Tatyana Sysoeva wrote: Hi! I heard a couple of times that use of cacodylate buffers in crystallization is bad, and not only because of the compound toxicity. As I understood, presence of the cacodylate in a protein crystal will cause a particular crystal degradation pattern upon X-ray exposure - "darkening of the crystals, gas formation" I tried to find some references on that and failed in doing so. I found some earlier discussions like this one: http://www.proteincrystallography.org/ccp4bb/message23691.html but don't have anything to reference in literature. I would appreciate if someone can point me to a right direction. I am sorry if this question is out of the groups topic range. Thank you in advance! Sincerely, Tanya -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure
Dear Tatyana, We once had a project where the crystallization condition contained cacodylate. The crystals diffracted to 1.9A and survived reasonably well under the beam (maybe there was indeed some colour change upon exposure, I do not remember exactly). We were working with drug soaks. The original structure is 1HYV. The most interesting result of cacodylate presence is modification of Cys residues. It was interpreted as S-dimethylarsinoyl cysteine. Best wishes, Sergei On 30-Jul-12 12:53 AM, Tatyana Sysoeva wrote: Hi! I heard a couple of times that use of cacodylate buffers in crystallization is bad, and not only because of the compound toxicity. As I understood, presence of the cacodylate in a protein crystal will cause a particular crystal degradation pattern upon X-ray exposure - "darkening of the crystals, gas formation" I tried to find some references on that and failed in doing so. I found some earlier discussions like this one: http://www.proteincrystallography.org/ccp4bb/message23691.html but don't have anything to reference in literature. I would appreciate if someone can point me to a right direction. I am sorry if this question is out of the groups topic range. Thank you in advance! Sincerely, Tanya -- Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven O&N2, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium Work phone: +32 16 330845 Fax: +32 16 323469 OR +32 16 323460 Mobile: +32 486 294132 Lab pages: http://pharm.kuleuven.be/anafar
Re: [ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure
Am 29 Jul 2012 um 18:53 hat Tatyana Sysoeva geschrieben: > > Hi! > > I heard a couple of times that use of cacodylate buffers in crystallization > is bad, and not only > because of the compound toxicity. > > As I understood, presence of the cacodylate in a protein crystal will cause a > particular crystal > degradation pattern upon X-ray exposure - "darkening of the crystals, gas > formation" > I tried to find some references on that and failed in doing so. > I found some earlier discussions like this one: > http://www.proteincrystallography.org/ccp4bb/message23691.html > but don't have anything to reference in literature. I would appreciate if > someone can point me to a > right direction. > > I am sorry if this question is out of the groups topic range. > > Thank you in advance! > Sincerely, > Tanya > Dear Tanya, cacodylate can be attacked by nucleophilic side chains and can form covalent adducts, e.g.: http://www.jbc.org/content/278/3/2008.long Good luck, Karsten --- Karsten Niefind University of Cologne Department of Chemistry Institute of Biochemistry Otto-Fischer-Str. 12-14 D-50674 Cologne Tel.: +49 221 470 6444 Fax: +49 221 470 3244
[ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure
Hi! I heard a couple of times that use of cacodylate buffers in crystallization is bad, and not only because of the compound toxicity. As I understood, presence of the cacodylate in a protein crystal will cause a particular crystal degradation pattern upon X-ray exposure - "darkening of the crystals, gas formation" I tried to find some references on that and failed in doing so. I found some earlier discussions like this one: http://www.proteincrystallography.org/ccp4bb/message23691.html but don't have anything to reference in literature. I would appreciate if someone can point me to a right direction. I am sorry if this question is out of the groups topic range. Thank you in advance! Sincerely, Tanya
