Content:
Introduction
This is a hopefully organised resource of anything we at Global Phasing could be doing related to the Covid-19 outbreak. Feel free to use anything found here - and let us know of any issues, problems or ideas.
Other resources
There is lot of very good information available for the MX structural community: please make use of those. Here are some to get you started:
To lear how to (re-)process deposited raw X-ray diffraction, see also our autoPROC example page.
Potentially relevant PDB structures
- CCP4 dictionaries were used if available (version 7.0.078)
- BUSTER refinements included LSSR NCS restraints, TLS refinement and automatic water update
- initial refinements were done fully automatic without any user intervention (unless stated otherwise on the relevant sub-page)
Please remember that none of these results are in any way supposed to provide the best/optimal refinement strategy: they have been done with a minimum of user intervention and it is very likely that other approaches, methods, software or users will come up with better interpretations. In cases where there could be a potential improvement on the original results, it is not meant as a critique of existing PDB depositions (which were done with the methods/software available at the time and sometimes under immense pressure): we are very grateful for all authors making their models and data available through the wwPDB!
The following list(s) are (mainly) based on
- Joyce, M.G., Sankhala, R.S., Chen, W.H., Choe, M., Bai, H., Hajduczki, A., Yan, L., Sterling, S.L., Peterson, C., Green, E.C. and Smith, C., 2020. A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein. bioRxiv. (Table S2).
- a Google Scholar search for "PDB (Covid-19 OR OR SARS-CoV)"
(Re-)refinements with BUSTER
Notes:
- 20200319: PDB entries 5R7Z, 5R80 and 5R83 were transformed to the more conventional (and consistent) C2 cell setting by re-indexing the deposited reflection data according to (h,k,l) -> (h+2l,k,-h-l).