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?
>
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