Hi folks
just my two ha’porth.
Back in the mid 1990s, when MAD was becoming common and tunable beamlines were
being installed at every synchrotron you could shake a stick at, I was involved
in several successful projects involving 5-Br-U in oligo-DNA crystallography.
In my (very, very) naïve hands at the time it worked like magic (I remember my
shock at seeing the base stacking in the first map I calculated for one of the
structures) - and this was using data collected on image plates with each image
spanning rather more than 1 degree - so not how it would be done now.
Since just about everything to do with data collection and processing and
structure solution has improved by leaps and bounds since then, I would back
Br-SAD to yield a structure.
If anyone’s interested, they can see my contribution regarding this at the 1997
CCP4 Study Weekend proceedings (this was prior to them appearing in Acta D),
available at -
https://legacy.ccp4.ac.uk/courses/proceedings/1997/h_powell/main.html
Contributions at the same meeting by others whose names will be instantly
recognizable may well be more use than mine…
Best wishes
Harry
> On 19 Sep 2023, at 19:32, Wagner, Armin (DLSLtd,RAL,LSCI)
> <0000ada38eff8538-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> 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
>
########################################################################
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/
