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

Bruno KLAHOLZ klaholz at igbmc.fr
Tue Apr 27 12:33:48 PDT 2021


Hi Matthias,

what is the space group?
It may help to work with a lower symmetry (i.e. that could remove the 2-fold symmetry axis going through the middle of your dimer), which may give for example 2 molecules in the asymetric unit, and instead refine this with non-crystallographic symmetry (NCS) restraints.

Best,

Bruno


###########################################################################
Bruno P. Klaholz
Centre for Integrative Biology
Department of Integrated Structural Biology
Institute of Genetics and of Molecular and Cellular Biology 
67404 ILLKIRCH CEDEX
FRANCE
http://www.igbmc.fr/Klaholz
http://www.igbmc.fr/grandesstructures/cbi
http://frisbi.eu
http://instruct-eric.com
https://inext-discovery.eu

-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Matthias Uthoff
Sent: 27 April 2021 18:01
To: phenixbb at phenix-online.org
Subject: [phenixbb] Refinement of a b-Strand swapped into the sheet of the symmetry related copy

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

-- 
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
Internet:http://px.uni-koeln.de

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