I agree that everything seems to be fine. It looks like a crystal with
higher-than-average solvent content, but the crystal lattice is present
and, based on the description, there is no indication of other problems,
except for the unexplained densities (I will come back to those later).
BTW, those channels are not unusually large. For elongated molecules, as
in this case, 60-80% solvent content is not uncommon if they pack
through end-to-end contacts.
The most important point is that R and R-free indicate the current model
explains the ASU content well. If large portions of the model were
missing, both values would not be this low. So, whatever those densities
represent, they are unlikely to correspond to an entirely new molecule.
To me, the difference density looks more like water/solvent/small
molecules. There is more of this density in the "corners" of the lattice
simply because there is a greater chance for such molecules to be
ordered where there is a higher local density of potential interactors.
At the same time, because the molecule is a helical bundle, surface
(channel) -facing side chains can be quite flexible, which may lead to
multiple conformations for solvent molecules coordinated on the surface,
which would create such elongated density.
Also, with the high solvent content and that type of packing, it is
possible that some solvent molecules in the channels are well- or
semi-ordered beyond the first solvation layer (in particular in those
corners). At 2.0-2.5 A resolution, we expect 0.5-1 water per aa in the
model, and I would expect for this lattice to see closer to ~1 water
molecule/aa.
How many water molecules are currently included in the model?
Best regards,
Dominika
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 Alejandro
Buschiazzo
Sent: Friday, February 6, 2026 8:31 AM
To: [email protected]
Subject: Re: [ccp4bb] Crystal pathology diagnosis please
On 6 Feb 2026, at 11:12 AM, Catherine Back <[email protected]> wrote:
Hi All,
Thank you so much to everyone for all the suggestions so far. In reply:
* The density appears to form a contiguous gap in the lattice (see image
attached). The channel just looks too big to be real (in my opinion).
Why "too" big?
If crystal contacts are there, and hold the crystal together, it may be
a case of particularly high solvent content (there are several examples
reported)
* I didn't loop/freeze the crystals so I can't tell you if they were
soft/fragile, but no one mentioned that to me.
* Apologies for not mentioning - the res of the initially solved structure =
2.3 Å. R factors for the almost complete structure were 0.22/0.27.
These numbers, very roughly of course, sound like there's nothing
especially wrong with this model/structure.
Not saying that you shouldn't look for alternative space groups and/or
better processing! Other colleagues have suggested very interesting
approaches to do that.
...but, maybe also keep an open mind as to the fact that your processing
is OK, and that you REALLY have huge solvent channels in this crystal.
* <...snipped...>
* Contour level was probably around 1.
....again, maybe play around lowering this! Just to see whether you can
make any sense of those Fo-Fc positive peaks (that seem like
connected/continuous density) close to your current model.
Do you have extra fragment(s) in your protein sequence that has(ve) not
been modeled?
Good luck!
Alejandro
* <...snipped...>
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