[phenixbb] Refinement of a b-Strand swapped into the sheet of the symmetry related copy

Boaz Shaanan bshaanan at bgu.ac.il
Tue Apr 27 09:19:05 PDT 2021

Do you really need those restraints to maintain the integrity of the beta sheet at 3 ang. resolution?

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel

On Apr 27, 2021 19:04, Matthias Uthoff <matthias.uthoff at uni-koeln.de> wrote:
Hi phenixbb,

I am working on a homodimer. Each protein has an internal b-sheet with
three b-strands, however the sheets swap their middle strands. So a
sheet consists of one strand from molecule A surrounded by two strands
from molecule B or vice versa. As I am at 3 A resolution, I would like
to set secondary structure restraints including correct hydrogen bonding
between the strands of the two molecules.

My problem: There is only one protein in the ASU and the "other"
molecule is in deed just a symmetry mate.

Phenix is not able to automatically detect this and if I provide the
restraints myself, phenix discards them as it is falsely assuming the
b-sheet is intramolecularly (all on chain A) and hence the strands are
30ish A apart.

What is the best way of refining this feature?

Thanks in advance,


Matthias Uthoff, PhD Student

University of Cologne
Institute for Biochemistry
Zülpicher Straße 47
D-50674 Cologne

Phone: +49 221 470 3211
E-Mail:matthias.uthoff at uni-koeln.de

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