Hello,
This density is the 'evil sausage-like blobule' that tends to crop up
whenever something ill-defined (but sausage-like) binds weakly to the
surface of the protein. It could be almost anything - something from the
polyacrylic acid, something from Triton (it has lots of sausage-like
shapes), or perhaps a chain of poorly ordered and incompletely occupied
waters.
I would leave this density unfilled and mention it briefly in the
description of the structure. Alternatively you could model this as
disordered water and again, briefly mention this treatment in the
"results".
Good luck,
Artem
> Hi all,
>
> I have a 1.8A structure for which I am in the final stages of refinement.
> In a critical hinge region there are two unknown molecules bound to my
> protein, which appear to induce the formation of a domain swap. I am
> totally out of ideas as to what this molecule could be. I have attached a
> a jpg of the offending region. The total length of the unknown molecule is
> ~4.4A. The environment is polar and solvent exposed.
>
> The crystallisation condition was: 0.1 M HEPES, 18% polacrylic acid,
> MgCl2, pH 7.0. Cryoprotectant was 20% glycerol. I wish it hadn't been, but
> triton-X was used during cell lysis as were Roche Complete Mini Protease
> Inhibitor Cocktail Tablets.
>
> Glycerol is of the correct length but after one round of refinement a
> strong negative difference density appears over the middle -OH group and R
> factors increase. In addition, any molecule which is alkane-based has
> serious clashes with the protein backbone (eg. glycerol or ethylene
> glycol, C2H6O2).
>
> Has anyone seen similarly shaped density, or have any ideas what it could
> be?
>
> Thanks a lot for your help guys, I'm very grateful for any suggestions.
> All the best,
> Miriam
>
> PS. Also thanks to everyone who writes in publicly to the bb - it has been
> a great learning resource!
>
>
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