Isn't there something about scattering factors being ... difficult...
for CryoEM reconstructions?
Which I imagine would cause issues in refinement.
Frank
On 25/07/2025 12:35, 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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