[phenixbb] Peptide bond to symmetry related molecule

Damian Ekiert damian.ekiert at ekiertlab.org
Mon Aug 23 07:16:01 PDT 2021

Hi All,

We are refining several structures in which the N-terminal residue of chain A appears to form a peptide bond to the C-terminal residue of its symmetry mate, chain A. In reality, the target protein consists of 4 identical helical repeats that pack end to end. Slippage and averaging over the 4 possible registers leads to the appearance of an infinitely long polymer in the crystal, with no breaks between protomers.

Is it possible to enforce a peptide bond to symmetry mates in Phenix, and what is the easiest way to do this? I have found a several cases in the archives on how to deal with symmetry clashes, but struggling to figure out how to deal with a peptide bond.

Thanks for your help!



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Damian Ekiert
Assistant Professor
Skirball Institute | NYU School of Medicine
Depts. Cell Biology and Microbiology
damian.ekiert at ekiertlab.org

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