Figure 5: MEM refinement of the structure of 3c.
From: Protein encapsulation within synthetic molecular hosts
(a) The crystal structure of 3c. Only the M12L24 spherical shell was modelled by conventional crystallographic analysis. Within the 3c shell, the MEM-refined electron density ascribable to ubiquitin was mapped (red: 0.35 eÅ−3, a value determined by electron density histogram analysis; white: 0.39 eÅ−3, a typical electron density of protein). (b) The combination of the crystal structure of 3c and the modelling of a ubiquitin molecule. (c) The difference in the electron density histogram between ubiquitin-containing sphere 3c and empty sphere 5c is shown. A positive narrow peak at 0.35 eÅ−3 (blue) and a negative broad peak at around 0.29 eÅ−3 (green) are observed. The positive peak is close to the typical electron density of proteins (0.39 eÅ−3) and thus attributed to the ubiquitin electron density. The negative peak is consistent with the value of 0.29–0.35 eÅ−3 for the DMSO–isopropyl acetate mixed solvent. Thus, the histogram difference clearly shows the presence of ubiquitin and the exclusion of solvents in the void of 3c. For further details, see Supporting Online Materials. Inset: a picture of the crystals of 3c.
