Hi Kavya, As others have mentioned, the unit cell is too small to contain your protein. With a volume of ~4820 Ang^3, the unit cell can contain at most ~268 atoms, excluding hydrogens (divide the volume by 18 to get this number). If the symmetry is P3, then the asymmetric unit can only contain ~89 atoms (divide the number of atoms in the unit cell by 3), which is not a lot. It is most likely something organic from your buffers (the ligand, TCEP, protein fragment, other buffer components, etc).
Searching the CCDC (https://www.ccdc.cam.ac.uk/structures/?) or the COD ( https://nanocrystallography.org/search.html) databases may be helpful. The CCDC also has a unit cell searcher tool (CellCheckCSD) that you can download and use without a license ( https://www.ccdc.cam.ac.uk/support-and-resources/downloads/). Collecting higher resolution data (<1 Ang) and trying to solve this with SHELXT would likely get to the bottom of things if you really want to know. Best of luck! Kind regards, Jessica On Fri, Feb 3, 2023 at 7:37 AM Artem Evdokimov <artem.evdoki...@gmail.com> wrote: > With 50 mM Zn++ in solution, whatever it is will probably have a Zn salt > in it. So if you wanted to solve it by direct methods or via SAD - that > should do well. Sadly (hur hur) it's probably quite small, whatever it is. > > Artem > > - Cosmic Cats approve of this message > > > On Fri, Feb 3, 2023 at 6:20 AM Mark J. van Raaij <mjvanra...@cnb.csic.es> > wrote: > >> like others mentioned, looks like something in between a salt and a >> protein, perhaps TCEP, the ligand, a peptide cleaved from your protein by >> trace protease. >> If possible, I would move the detector closer, collect an atomic >> resolution dataset and try to solve the structure by direct methods. You >> never know, it could be something interesting. >> >> Mark J 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) >> Section Editor Acta Crystallographica F >> https://journals.iucr.org/f/ >> https://namedrop.io/markvanraaij >> >> On 3 Feb 2023, at 09:22, kavyashreem <kavyashr...@instem.res.in> wrote: >> >> Dear all, >> >> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the >> condition 10%PEG3350, 50mM Zinc acetate. >> >> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH >> 8. >> >> Crystal: Crystal: >> crystal under UV m >> >> <b06fc576.png> <e091c7fd.png> <8ef9453e.png> >> >> When we collected the data at an in-house facility, it looked something >> like this: >> >> <b903961d.png> >> >> The minimum resolution spot is around 9Ang and maximum ~2.2Ang. >> >> I have not come across a protein diffraction like this, nor of a salt. >> When I ran the gel for the incubated protein (protein+ligand), there was no >> degradation. >> >> Although, I was sure there is some problem with this image I tried >> processing, which could not be, But indexing showed a unit cell of 11Ang, >> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not >> the third. >> >> Can anyone please shed some light on this diffraction image? >> >> How can it happen? >> >> >> Thank you >> >> Regards >> >> Kavya >> >> >> ------------------------------ >> >> 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 > ######################################################################## 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/
