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The lattice parameters of the average structure are strongly affected by the regularity of the stacking sequence, i.e., by the volume fraction of the two-layer nanotwins and their distribution.
Time-averaged residue-based Root Mean Square Fluctuations (RMSF), calculated after alignment of the MD generated structures with the average structure, are color-mapped onto the protein structures in Fig. 5.
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The shape of the average structure is similar to what is expected from the current structural model (Worrall et al., 2011); the main components of the basal body were assigned as YscC and YscDJ rings following this nomenclature and the secretin YscC was assumed inserted into the outer membrane.
The average structure was separated into COMP (UNAcP-NAG), LIG (NAGs) and PTN (UNAcP), and each was, finally, optimized again.
The energy-minimized average structure was chosen as the MMDS-refined 3D model.
An average structure was obtained with Weatsheaf (25).
These nine structures were averaged, and the resulting average structure was subjected to complete relaxation matrix analysis.
The average structure is a combination of the two settings, and this combination is C-centered.
Thus, the average structure was in good agreement with the observed NOE intensities.
An average structure was further refined using a steepest descent energy minimization.
So, a representative average structure was generated for this time period.
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