Dear All, We have a rather confusion situation currently with our designer proteins. They are highly symmetric and consist of identical amino acid repeats in tandem that are organized in 3D around a central (rotation axis). Our first series of proteins like this was the Pizza (3ww9) which crystallized in P212121.
However for other proteins we have now a bit of a problem. After crystallization of our new proteins some of them crystallized in such a way that we can solve the structure with such a symmetry that only a fragment of the protein is present. For instance we only see 2 repeats in the asymmetric unit but in fact in the monomeric structure there should be 8. The 8fold symmetric protein can be reconstructed from crystal symmetry. My question is now. Should we solve and deposit this crystal structure to the most symmetrical smallest asymmetric unit resulting in an incomplete protein in the asymmetric unit or should we solve the structure in a lower space group such that the asymmetric unit contains a full length monomeric protein. The protein has additional few amino acids at N-terminal but we can not see these regions on electronic density map. When comparing the two R free we see that the lowest spacegroup has a slightly better (4%) R free value than the higher spacegroup with an incomplete protein in the asymmetric unit. The PDB document (https://cdn.rcsb.org/wwpdb/docs/documentation/annotation/wwPDB-A-2017Aug02-V2.8.pdf) is described, "The asymmetric unit may be one molecule or one subunit of a multimeric protein, but it can also be more than one." on page 34. So should we go for the highest symmetry as observed from the diffraction data, or go for a lower symmetry agreeing with a full protein. Thank you for you help. Kindest Regards, Hiroki noguchi KU LEUVEN, Belgium
