After simultaneous IQP fitting, the lowest RMS error for the fitted structure is 8.6 Å with respect to the crystal structure, and only slightly larger than our results observed for simulated maps.
Personally, I loved the more delicate, fitted structure above the waist followed by a long, dramatic silhouette a la Badgley Mischka.
For example, the best fitted structure of the four-component assembly 2BO9 has an RMS error of 1.7 Å.
Contacts between the E1 and E2 glycoproteins were determined (Materials and Methods) for the T = 4 fitted structure and compared with the improved, independently fitted, domain structure (Table 6).
Once f has been determined, the full embedding space is warped and the atomic positions of the fitted structure are mapped accordingly.
The fitted structure is the stigmatellin-bound form, but the Rieske domains also protruded from the map when the uninhibited form was used instead (not shown).
Additionally, the orientation of cytochrome c in the cryo-EM fitted structure of apoptosome [PDB: 3J2T] [ 25] was also treated as a model under investigation.
Moreover, intramolecular disulphide cross-links engineered between AAA-1 and motif 2 residues in TthClpB, EcoClpB and yeast Hsp104 are also compatible with the fitted structure.
We then monitored the system for convergence by calculating the root mean squared deviation between the coordinates of the fitted structure and the starting model.
Particularly striking was the increase in hydrophobic contacts in the independently fitted results, which demonstrated how the heterodimer adapted itself to the quasi-equivalent symmetry of the VLPs compared to the constraints imposed by the crystal lattice.> -wrap-foot> Unlike the T = 4 fitted structure, the independently fitted structure lacked exact symmetry between the i3 and q3 spikes.
