Hi all, Since some emails were not REPLY ALL, I have answered them here: The structure solved with MR; high sequence identity. Disorder occurs only when ligand is bound. Model is almost 90 % complete except the disordered region. Please let me know if I can deposit structure as it is. I took example 1fcc (also low resolution). Seems many residues are outside Ramachandran plot (even Residue 266 has no density at all). Does it mean I can deposit this?
> Yes, it is okay to exclude few residues or even short stretches of > loops/helices/strands if there is no reliable/convincing electron density for > them even at low map contours because if there is no convincing density you > cannot reliably model the local structure. > > However, if you refine with tight NCS, which you probably should do at this > resolution unless there are significant differences in the 4 molecules, you > can also choose to keep residues for which there is no reliable density in > one of the molecules, provided those residues are well resolved in the other > molecules and refine well (density, B-factors). Also use TLS refinement. > > Irrespective of which of the 2 options you choose, make sure to add a remark > in the PDB header about the option chosen, so that others know what was done > and if you write it up in a manuscript, describe it there as well. > What is your R/Rfree currently? And what is the CC(1/2) of your data at 2.8 > If you haven’t done so already, I’d delete suspect, refine and see if > difference density comes back for it. The density looks similar to it. > Perhaps the domain is disordered and really needs to be deleted. > Other possibilities are that it is in an unexpected orientation or > conformation. > You may need several iterations of deleting, rebuilding and adapting. > > Were the input phases experimental or from a molecular replacement model, > and if the latter how complete was the model? > >
