Yes, but formal charge effects are not implemented. Last time I checked?
-James Holton
MAD scientist
On 7/25/2025 11:01 AM, Dominika Borek wrote:
I don’t think there’s anything particularly difficult about scattering
factors for cryoEM, but the patterns of dependences on atomic number
differs from that in X-ray crystallography. For instance, in X-ray
maps, oxygen atoms, common interactors of metal cations via carboxylic
acids and/or water molecules, appear “stronger” due to this
difference. Thus, at the same nominal resolution of ~2–3 A, the
coordination sphere in cryoEM maps looks less well-defined than in
X-ray crystallography maps (even though information content is the
same). I find the default restraints insufficient, so I apply
restraints manually in both Refmac/Servalcat and Phenix, e.g., I
define Mg2+ octahedral geometry with proper distances in a mini script
and include it in the refinement run. In other words, I vote for
tighter geometry.
D.
Dominika Borek, Ph.D. *** UT Southwestern Medical Center
5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
214-645-9577 (phone) *** 214-645-6353 (fax)
*From:*CCP4 bulletin board <[email protected]> *On Behalf Of
*Frank von Delft
*Sent:* Friday, July 25, 2025 10:10 AM
*To:* [email protected]
*Subject:* Re: [ccp4bb] Restraining metal sites in medium resolution
cryo-EM
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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