Hi Jessica, I am quite sure the protein cannot be fit in this unitcell. I was just curious why the diffraction has closely spaced spots.
Thanks On 2023-02-04 00:02, Jessica Bruhn wrote: > 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 ######################################################################## 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/
