At high resolution I'd still put the restraints in, with higher
variance, so the geometry is still correctly reproduced in the PDB/CIF file.
But apropos actual geometry:
> The other option is that the restraints need to be up-weighted so that
> they have more parity with the protein bond restraints and other
> targets that one might use.
This assumes they are as well-characterized as protein values, or as
stiff as a Calpha-Cbeta bond.
> number, and bond length/angles are quite well known.
Frequently not a simple length, for example see:
Bazayeva et al 2004 "A database overview of metal-coordination
distances in metalloproteins"
https://pmc.ncbi.nlm.nih.gov/articles/PMC11066882/
where any number of metal-ligand distances are not single-valued.
This was my experience recently where at least one restraint offered up
by phenix.metal_coordination was rather at odds with the actual
well-defined separation in the high resolution map.
Phil Jeffrey
Princeton
On 7/25/25 7:35 AM, Matthew Snee wrote:
Hi Everyone
Id let to get the communities opinions on metal sites in Cryo-EM models.
In X-ray structures the geometry of metal coordination (when restrained
correctly) looks pretty good, even in low resolution structures, and at
very high resolution you may wish to avoid applying restraints so that
the precise coordination distances/angles can tell you something about
the physical chemistry of the system (I.E reduction state of catalytic
metals in chemical biology). I have found that EM structures between
2-3Å which are good enough to see individual features (un ambiguous
sidechain rotamers and coordinated waters in the metal complex)
refinement outputs don't look nearly as nice.
My question is this,:
Is this just "the way it is" because the optical resolution and true
atomic resolvability is different between X-ray and EM.
The constraints of the crystal might help to collapse the conformational
landscape somewhat, and solvent flattening might repress (unidentifable)
minor states that would distort the real-space fit, thus improving the
convergence between ideal geometry and fit to the density.
EM structures that have very high resolution FSC cutoffs can still be
distorted by minor anisotropic flexibility in one or more particular
direction, there are ways to isotropise maps, but I dont really like
refining against these.
The other option is that the restraints need to be up-weighted so that
they have more parity with the protein bond restraints and other targets
that one might use.
Basically, are these structures where the coordination geometry is
almost certainly not completely correct, likely to be better, more
useful, or closer to the "true structure" or is it better to enforce the
geometry more strictly than you would for an equivalent X-ray structure
in order to achieve the most likely sensible cluster.
I dont think either approach is "wrong" because you could make an
argument for building what you see, only building the links that are
directly suggested and restraining them as best you can, I'm not a
metal cluster expert by any means, but I do know that the coordination
number, and bond length/angles are quite well known.
I know this is potentially more of a CCPEM/Phenix query, but X-ray
people are generally more involved in the physical chemistry side (I
know not always 🙂!),
Best wishes
*Matthew Snee, PhD*
Post-doctoral Research Associate
The Baldock Lab | Michael Smith Building C3.214 | Wellcome Trust Centre
for Cell-Matrix Research |Division of Cell Matrix Biology & Regenerative
Medicine| School of Biological Sciences| Faculty of Biology, Medicine
and Health, University of Manchester, Oxford Road, Manchester M13 9PT
Lab Tel: +44 (0)161 306 2869
cell-matrix-research
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