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) 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 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) and Ca could be attractive as a potential anomalous scatter as well. Best regards, Armin From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Mark J. van Raaij <mjvanra...@cnb.csic.es> Date: Tuesday, 19 September 2023 at 12:31 To: CCP4BB@JISCMAIL.AC.UK <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 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> 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> 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> 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> 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> 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 -- ---------------------------------------------------------- "Live Simply and do Serious Things .. " - Dorothy Mary Crowfoot Hodgkin OM, FRS "In Science truth always wins" - Max Ferdinand Perutz OM FRS ---------------------------------------------------------- Dr. Ramanathan Natesh Associate Professor, School of Biology and Center for High-Performance Computing (CHPC), Founding and Current President of Cryo Electron Microscopy and 3 Dimensional Image Processing Society of India (CEM3DIPSI), Indian Institute of Science Education and Research Thiruvananthapuram (IISER-TVM), Maruthamala P.O., Vithura, Thiruvananthapuram, 695551, Kerala, India nat...@iisertvm.ac.in http://faculty.iisertvm.ac.in/natesh Researcher ID: http://www.researcherid.com/rid/C-4488-2008 ORCID: http://orcid.org/0000-0002-1145-5962 Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134 PUBLONS: https://publons.com/author/1520837/ramanathan-natesh#profile Office Ph. 0091- 471-2778087 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
