[phenixbb] Refinement using a homolog as a reference

Joshi, Amar (Dr.) aj180 at leicester.ac.uk
Thu Jul 25 01:44:54 PDT 2013


I am refining ligand-protein complexes at 3.2Å dataset with a human protein. My Rfree is ~0.34 but my ramachandran stats are concerning me: 85% favoured, 4.5% disallowed.

The structure of a yeast homolog has been deposited at 2.4Å resolution. The yeast structure contains additional loops but is ~55% identical to the human protein. The overall conformation between the homologs is very similar.

Can I use this as a reference model? Should I prune the reference model? Will different numbering schemes affect the refinement?

Many thanks,

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