I have also found that there is significant anomalous signal from strontium near the Se K-edge, which is useful if one uses strontium chloride instead of potassium chloride (or in addition to KCl) during crystal growth.
Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu> (214) 645-6383 (phone) (214) 645-6353 (fax) On Sep 19, 2023, at 1:32 PM, Wagner, Armin (DLSLtd,RAL,LSCI) <0000ada38eff8538-dmarc-requ...@jiscmail.ac.uk<mailto:0000ada38eff8538-dmarc-requ...@jiscmail.ac.uk>> wrote: EXTERNAL MAIL Dear Fu Xingke, Indeed P-SAD is quite attractive but requires high resolution as the number of anomalous scatterers (1 P per nucleotide) is rather large, but the unit cells are typically quite small, resulting in a rather small number of anomalous differences per scatterer. Based on the very nice publication from Tom Terwilliger et al. ( https://doi.org/10.1107/S2059798315019269<https://urldefense.com/v3/__https://doi.org/10.1107/S2059798315019269__;!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowSdSNrDrk$>) we wrote a little web app to predict the success for S-SAD phasing at the long-wavelength beamline I23 at Diamond. https://www.diamond.ac.uk/Instruments/Mx/I23/resolution-requirement-phasing-app.html<https://urldefense.com/v3/__https://www.diamond.ac.uk/Instruments/Mx/I23/resolution-requirement-phasing-app.html__;!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowSvD5csvg$> While the predictions are pretty reliable for S-SAD, there is a (not heavily tested) option to also submit DNA or RNA sequences, which can give you a hint on what you are against, or what resolution you should aim for. Unfortunately, we have not had many successful examples to far, but basically all the P-SAD projects which were predicted not to work at the resolutions the crystals diffracted to didn’t solve, so we are very interested in projects which are predicted to work to fine tune this also for P-SAD as there will be continuous need for experimental phasing in particular for non-canonical RNA/DNA structures. 5-Br-U is a good alternative and works well, but we have also managed to solve RNA/DNA by K-SAD or Co-SAD (https://doi.org/10.1093/nar/gkaa439<https://urldefense.com/v3/__https://doi.org/10.1093/nar/gkaa439__;!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowSr-TWaw8$>) and Ca could be attractive as a potential anomalous scatter as well. Best regards, Armin From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Mark J. van Raaij <mjvanra...@cnb.csic.es<mailto:mjvanra...@cnb.csic.es>> Date: Tuesday, 19 September 2023 at 12:31 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] the structures of Nucleic acid This just appeared and may be relevant: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628<https://urldefense.com/v3/__https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628__;!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowSyfBOklU$> Critical Reviews and Perspectives When will RNA get its AlphaFold moment? Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) On 18 Sep 2023, at 18:07, William G. Scott <00002844d921eb97-dmarc-requ...@jiscmail.ac.uk<mailto:00002844d921eb97-dmarc-requ...@jiscmail.ac.uk>> wrote: The phosphorus absorption edge is about 5.8Å. I've had much better luck with 5-Br-U for anomalous phasing. Molecular replacement with sub-structural fragments can also work: <https://scottlab.ucsc.edu/scottlab/reprints/2010_Scott_Methods.pdf><https://urldefense.com/v3/__https://scottlab.ucsc.edu/scottlab/reprints/2010_Scott_Methods.pdf*3E__;JQ!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowS8KUir6c$> Yours sincerely, William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA On Sep 18, 2023, at 2:43 AM, Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote: I am afraid most scientists will use the most straightforward technique! If SAD is available the PHOSPHATE backbone of DNA will provide sufficient signal to allow SAD to work, and you get an unambiguous answer to whether it is A-DNA or B or Z... MR will usually work of course as well Eleanor On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan <nat...@iisertvm.ac.in<mailto:nat...@iisertvm.ac.in>> wrote: Dear Fu Xingke, Depends on what Nucleic Acid you are talking of. If it is RNA, you can expect some sequence to tertiary structure correspondence so you might be able to try more MR as compared to DNA. DNA may have double helical architecture but less sequence to tertiary structure correspondence, and hence DNA is less likely to have a 3D structure like RNA specific structure for a sequence. SAD has become a straight forward method to avoid all these problems to get ab-initio structure. So many go for it directly. Hope that helps. Best wishes, Natesh On Mon, 18 Sept 2023 at 13:36, fuxingke <fuxingke0...@163.com<mailto:fuxingke0...@163.com>> wrote: Dear Colleagues, Reacently, I find the structures of Nucleic acid are solved by single-wavelength anomalous diffraction(SAD). So, why molecular replacement (MR) not? Regards Best wishes, Fu Xingke Institute of Physics CAS To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!FVcv4z-85T4vC7VbHq9ovFGb90t3epudF1WV4ZvkXWqf51jVB7EfNZAHkQnf77TODeUSY5TVKsfEQoPZFt8d0q4Ldoubul1hBmZxnowS_wNzuHE$> -- ---------------------------------------------------------- "Live Simply and do Serious Things .. 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