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CCP4BB  March 2020

CCP4BB March 2020

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Subject:

Raw diffraction images for SARS-CoV-2 related structures

From:

Gerard Bricogne <[log in to unmask]>

Reply-To:

Gerard Bricogne <[log in to unmask]>

Date:

Fri, 27 Mar 2020 19:26:05 +0000

Content-Type:

text/plain

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text/plain (193 lines)

Dear all,

     It is a pleasure to be able to end the (GMT) week by calling for a huge
round of applause for the Diamond team, who this afternoon started uploading
a large collection of sets of raw diffraction images (77 as we write but the
upload is still ongoing) for PDB entries that were released two days ago.

     Special thanks to Graeme Winter who organised the upload to Zenodo. The
datasets are collectively accessible via the following link:

https://zenodo.org/search?page=1&size=20&q=keywords:%22SARS-CoV-2%20main%20protease%22

     Graeme asked that "major kudos [be given] to Zenodo developers who have
been very responsive with helping us do automated downloads".

     Happy scrutiny and reprocessing of these datasets, and re-refinement of
the associated structures, to all hard-core MX addicts!


     With best wishes,

     Clemens & Gerard.

--
On Thu, Mar 19, 2020 at 10:00:11AM +0000, John Berrisford wrote:
> Dear all
> 
> The wwPDB OneDep system allows depositors to provide DOIs of raw
> diffraction images during deposition to the PDB and once again
> encourages depositors to provide a DOI for raw images when they have
> submitted.  
> 
> Out of the 9665 X-ray entries that were released in 2019 we have DOI's
> for raw images in 205 of these entries.  
> 
> We would encourage depositors to provide the DOI for their raw images
> when they are available.  
> 
> Regards
> 
> John
> 
> 
> On Mar 19 2020, at 9:48 am, Joel Sussman <[log in to unmask]> wrote:
> 
> > 19-Mar-2020
> > Dear Loes, Peter, Clemens & Gerard,
> > I concur that it is crucial to preserve the original diffraction data
> > and make it available to anyone who would like to use it.
> > As an example, please see the very recent paper by 
> > Nachon et al (2020). "A second look at the crystal structures of
> > Drosophila melanogaster acetylcholinesterase in complex with tacrine
> > derivatives provides Insights concerning catalytic intermediates and
> > the design of specific insecticides" Molecules 25 pii: E1198 
> > [https://www.ncbi.nlm.nih.gov/pubmed/32155891].
> > The study reexamines the original data, with modern software tools,
> > the original data of a paper we published in 2000 (~20 years ago) and
> > revealed features that had not been noticed. Specifically 
> > 1) previously unmodeled density in the native active site can be
> > interpreted as stable acetylation of the catalytic serine. 
> > 2) Similarly, a strong density in the DmAChE/ZA complex, originally
> > attributed to a sulfate ion, is better interpreted as a small molecule
> > that is covalently bound. The complex is reminiscent of the
> > carboxylate/BChE complexes observed in crystal structures of hBChE
> > [Brazzolotto et al, 2012; Nicolet et al, 2003], and demonstrates the
> > remarkable ability of ChEs to stabilize covalent complexes with carboxylates.
> > Thus, the study demonstrates that updated processing of older
> > diffraction images, and the re-refinement of older diffraction data,
> > can produce valuable information that could not be detected in the
> > original analysis, and strongly supports the preservation of the
> > diffraction images in public data banks.
> > Best regards
> > Joel
> > ------------------------------------------------------------------------------------
> > Prof. Joel L. Sussman.        [log in to unmask]   www.weizmann.ac.il/~joel
> > Dept. of Structural Biology   tel: +972  (8) 934 6309       proteopedia.org
> > Weizmann Institute of Science fax: +972  (8) 934 6312
> > Rehovot 76100 ISRAEL          mob: +972 (50) 510 9600
> > -------------------------------------------------------------------------------------
> >  
> >  
> >> On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes)
> >> <[log in to unmask]> wrote:
> >>  
> >> Dear Gerard,
> >>  
> >> This is a great idea. Of course I am very much in favour of making
> >> available raw diffraction images, and such a virtual workshop could
> >> demonstrate the usefulness of reprocessing raw diffraction data and
> >> structural refinements. I am not at all afraid that archiving of raw
> >> data that are the basis of a scientific paper will have significant
> >> environmental effects: this is minor compared to our everyday use of
> >> cloud services.  And as Graeme mentioned: when archiving raw data
> >> make sure to add sufficient and correct meta data.
> >>  
> >> Best wishes,
> >> Loes
> >>  
> >> ___________________________________________________________
> >> Dr. Loes Kroon-Batenburg
> >> Dept. of Crystal and Structural Chemistry
> >> Bijvoet Center for Biomolecular Research
> >> Utrecht University
> >> Padualaan 8, 3584 CH Utrecht
> >> The Netherlands
> >>  
> >> E-mail : [log in to unmask]
> >> phone  : +31-30-2532865
> >> fax    : +31-30-2533940
> >>  
> >> Van: CCP4 bulletin board <[log in to unmask]> namens Gerard
> >> Bricogne <[log in to unmask]>
> >> Verzonden: woensdag 18 maart 2020 23:30
> >> Aan: [log in to unmask] <[log in to unmask]>
> >> Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
> >>  
> >> Dear colleagues,
> >>  
> >> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
> >> structures in the PDB seems to indicate that that there might be potential
> >> to improve these if refinements could be repeated after some reprocessing
> >> and further analysis of the raw diffraction images, rather than
> >> against the
> >> deposited merged data. This statement should in no way be construed
> >> as a
> >> criticism of the remarkable achievements of the research groups concerned,
> >> who have been operating under tremendous time pressure, but as an exciting
> >> opportunity to push methods to their limits on a uniquely significant class
> >> of structures.
> >>  
> >> Another consideration is that the various logistical problems created by
> >> COVID-19 may soon make it increasingly difficult to collect new diffraction
> >> data on potential drug targets relevant to the fight against SARS-CoV-2,
> >> underlining the importance of ensuring that the best results be obtained
> >> from every dataset actually collected, and that the most useful conclusions
> >> be drawn from the analysis of those datasets towards improving the quality
> >> of subsequent data collections. 
> >>  
> >> On this basis we would like to propose that special efforts be made
> >> to grant
> >> public access to the raw image data associated with any SARS-CoV-2 related
> >> structure that is deposited into the PDB. This can be done by (1) archiving
> >> these raw image data using resources such as data.sbgrid.org, zenodo.org,
> >> proteindiffraction.org or any other cloud-based data-sharing service, and
> >> (2) communicating the corresponding DOIs to the wwPDB centres. This idea
> >> could be extended to datasets that investigators would like to offer to
> >> interested methods developers or expert users at the pre-deposition stage.
> >>  
> >> Experts making use of those raw data would be encouraged to document,
> >> in as
> >> much detail as possible, how particular programs or workflows could
> >> be used
> >> on those structures/datasets to obtain the best results. This would
> >> be a
> >> kind of "virtual workshop", a particularly valuable collective
> >> activity at
> >> the present time when several in-person workshops (e.g. RapiData)
> >> have been
> >> cancelled and many meetings are in limbo for several months.
> >>  
> >> The latter activity would benefit from having a centralised facility
> >> set up
> >> for the experts to post their results and annotations: we could
> >> create such
> >> a facility, but other, larger groups might want to consider doing so. 
> >>  
> >>  
> >> With best wishes,
> >>  
> >> Clemens & Gerard.
> >>  
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