Hello,
go back to the basics:
_Burmeister, W. P_.
Structural changes in cryo-cooled protein crystals owed to radiation damage.
/Acta Cryst. D /*56*/, /328-341 (2000).
https://doi.org/10.1107/S0907444999016261
Wim
On 17/03/2025 17:03, Guillaume Gaullier wrote:
Hello,
Sorry to hijack this discussion, but does someone know if reduction of
a disulphide could be a manifestation of radiation damage? Especially
in cryoEM, since we're shooting electrons at it.
One way to test this would be to do a rough zero-dose extrapolation
(repeat motion correction with fewer and fewer frames, use the
particle coordinates and orientations determined with the full dose to
extract particle images and do reconstructions from the micrographs
obtained with fewer frames) and see if this feature appears with
accumulated dose. But this is tricky to do if motion correction is not
perfect. At least according to the paper that introduced HexAuFoil
grids: https://doi.org/10.1126/science.abb7927
<https://doi.org/10.1126/science.abb7927> ; but I don't know if anyone
has tried even without these grids.
Cheers,
Guillaume
------------------------------------------------------------------------
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Artem
Evdokimov <artem.evdoki...@gmail.com>
*Sent:* Monday, March 17, 2025 4:50:37 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Query Regarding Additional Density Near
Disulfide Bond in Cryo-EM Structure
To me this looks like a mixture of oxidized and reduced states of the
S-S bond. Hard to say with any certainty seeing as the (optical)
resolution is modest.
Artem
- Cosmic Cats approve of this message
On Mon, Mar 17, 2025 at 8:18 AM Devbrat Kumar <devformed...@gmail.com>
wrote:
Hello Everyone,
I am worried about the density of the disulfide bond in the
cryo-EM structure that I am analyzing. The experimental map shows
the expected density for the disulfide bond involving two cysteine
residues, but in addition, I see some unexplained density, which I
do not know how to interpret.
I have attached the figure for your reference. Does anyone have
experience with such extra density around a disulfide bond in
their structures? Any thoughts would be greatly appreciated.
Thanks for your attention and assistance.
Warm regards
Devbrat kumar
Postdoctoral Fellow
IITD, In
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Professor
Institut de Biologie Structurale (IBS) CIBB
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