[phenixbb] Refinement of a b-Strand swapped into the sheet of the symmetry related copy
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:
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
Phone: +49 221 470 3211
E-Mail:matthias.uthoff at uni-koeln.de
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