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