[phenixbb] [EXTERNAL] 3Fe4S clusters in real-space refinement

[Nigel Moriarty]

Rhys

You can use the phil option

superpose_ideal_ligand = *None all SF4 F3S DVT

to superpose an ideal F3S to avoid the mess. I'm also happy to take a
closer look.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909      Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464


On Mon, Apr 18, 2022 at 11:50 AM Edward Berry <berrye at upstate.edu> wrote:

> Have you seen:
> Iron–sulfur clusters have no right angles
> Nigel W. Moriarty and Paul D. Adams, Acta Cryst. (2019). D75, 16–20
> <http://journals.iucr.org/d/issues/2019/01/00/rr5165/index.html>
>
> The Phenix F3S library worked well for our Complex II structures a few
> years back. And those structures definitely confirm that the angles are not
> 90* for F3S. (FES Fe2S2 has close to right angles, I think)
> You have to be sure that the atoms are arranged in the same way as in the
> model or the restraints will try to invert your cluster;, and that the Cys
> ligands connect to the right irons.
> Ed
>
> Rhys Grinter wrote on 4/18/2022 12:24 AM:
> > Hi PHENIX BB,
> >
> > I'm currently refining a structure with 3Fe4S clusters into some high
> resolution cryoEM maps (1.57 Ang). However, refinement messes up the Fe4S
> cluster, by moving the existing Fe and S atoms into the wrong positions in
> the density.
> >
> > Is anyone aware of this issue and/or knows of a simple way to prevent
> this from happening?
> >
> > Cheers,
> >
> > Rhys
> >
> > --
> > Dr Rhys Grinter
> > Lab Head
> > Molecular Physiology of Microbial Pathogens (MP2) Lab
> > Monash University
> > +61 (0)3 9902 9213
> > +61 (0)403 896 767
> >
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