Does anyone know about protein crystals with a considerable percentage of the unit cell content (lets say more than 50%) occupied by disordered proteins? In my case it seems that the crystal is composed by ordered layers separated by 'void' space: my impression is that the void is another protein (linked to the ordered one by a couple of disulphide bridges) that is in multiple conformation and therefore appears to be disordered at the low resolution of the diffraction (3.14 A). Another simpler interpretation would be a wrong molecular replacement solution, but my impression is that the solution is correct (at the actual stage of refinement R/Rfree = 24/30%) modelling many loops that were not present in the search model.
Don't know about percentage, the abstract of Nature. 1976 Dec 2;264(5585):415-20. mentions that the Fc part of a Fab is disordered. (pdb 2IG2). I had the full paper at some time, but can't find it right now. So yes, it has been known to happen for some time.
I would try fitting a free-atom model (maybe with a poly-A sequence) and see if the density clears up (e.g arp/warp). And/or have a close look at your bulk solvent correction. Do your crystal contacts make sense? Could there be non-protein stuff (e.g. carbohydrates)?
24% at 3.14 seems almost too good.
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