Hi
I am also reminded that I was involved in the data collection but not structure
solution of a DNA cyclic octamer from a single wavelength dataset collected to
atomic resolution (on image plate…), which was solved after locating a Ba
(which turned out to be one of several with partial occupancy); the structure
solution was actually carried out in the laboratory of one G.M. Sheldrick,
using software that I think may have never been released to the public.
See
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC20809/
for details...
Harry
> On 19 Sep 2023, at 20:53, Diana Tomchick <[email protected]>
> wrote:
>
> 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
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>
>> On Sep 19, 2023, at 1:32 PM, Wagner, Armin (DLSLtd,RAL,LSCI)
>> <[email protected]> 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) 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 <[email protected]> on behalf of Mark J. van
>> Raaij <[email protected]>
>> Date: Tuesday, 19 September 2023 at 12:31
>> To: [email protected] <[email protected]>
>> 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
>> <[email protected]> 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
>> <[email protected]> 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 <[email protected]>
>> 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 <[email protected]> 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
>>
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