Hi Deepanshu, how complete the data set? What's completeness across resolution zones? Systematically missing reflections can have systematic impact in real space (maps). I've seen entire ligands or domains disappear due to missing low-resolution data.
Just another check-point to consider.. Good luck! Pavel On Wed, Oct 10, 2018 at 10:59 AM Deepanshu Choudhary < deepanshui...@gmail.com> wrote: > Dear all, > I am working on a protein complex. After many efforts, I obtained crystals > from one of the refinement screen (which took few weeks to grow) and I got > a 3 Å dataset at synchrotron. I scaled the dataset in P21 spacegroup (which > is also confirmed by Zanuda and Pointless). There is no twinning detected. > I solved the phase using molecular replacement with a model of over 90% > sequence identity. After several rounds of refinement with Refmac, the > Rfree is 0.307 and Rfactor of 0.23. > The density looks good and I can see everything that's important. But one > of the proteins has missing density in 2 of its beta strands (corresponding > to ~15%) and its not appearing upon several rounds of refinement. Also, the > B factors are higher for this protein. The missing beta strands are not at > the interface of the complex. > I ran some crystals on the gel and did silver staining to find both the > proteins and no degradation products. I doubt that there is any proteolytic > cleavage because the protein is unlikely to remain folded if those beta > strands are chopped out. > I want to ask if such a structure with missing density and high B-factors > (>100) can be deposited. Is it possible that some parts of the lattice > don't have this protein with missing density which is resulting in high B > factors? > I would appreciate your efforts if someone can send me few references > describing such type of structures. I would also welcome any other > suggestions and recommendations. > > Thanks and regards, > Deepanshu > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
