Hi Catherine,
It looks like the crystal is trapping some non-crystallized soluble
molecules inside those big channels (probably with occupancy lower than
1), really cool.
It would be amazing if you could use these crystals as a scaffold to
trap some protein that cannot be crystallized inside those channels with
high enough occupancy to solve their structure this way :)
BW,
D
On 06/02/2026 11:48, Catherine Back wrote:
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Morning All,
My colleague and I are trying to solve the structure of a long, alpha
helical bundle protein. We thought it had solved well with 2 molecules
in the AU (which had decent stats), but upon a closer look there are
very large 'solvent channels' in the lattice, with green/blue density
within. It looks like there are protein molecules, positioned
lengthways to the molecules in the AU, within these channels which the
autoprocessing (at Diamond Light Source) is not picking up. See images
attached.
I now have the image files and have been reprocessing them using
xia2-DIALS in ccp4i2.
I am unsure what kind of crystal pathology we're dealing with here.
There is no twinning warnings or anything else really that the
processing has identified. The space group is always identified as
P212121, unit cell 34.8, 184.8, 202.3, 90.0, 90.0, 90.0.
I've tried quite a few different things to get the software to fit
molecules into the density, including manually extending the unit
cell, but all the outputs have been wrong or had really bad stats. I'm
wondering if the indexing is wrong, but I'm not sure how to sort this.
There is clearly something going on here, which is either really
obvious (that I'm not identifying because I'm an idiot) or it's
something more complex.
Any ideas/help will be much appreciated.
Best wishes,
Catherine Back
Dr Catherine R. Back (she/her)
Senior Post-doctoral Research Associate
School of Biochemistry
University of Bristol
UK
[email protected]
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