R-type straight flagellar filament made of full-length flagellin
ELECTRON MICROSCOPY
Sample
R-TYPE STRAIGHT FLAGELLAR FILAMENT
Specimen Preparation
Sample Aggregation State
FILAMENT
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
102
Reported Resolution (Å)
4
Resolution Method
Other Details
The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then ...
The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then, initial model of full-length flagellin was built by tracing missing terminal chains. The model was refined using both positional and simulated annealing refinements, by a molecular dynamics refinement program, FEX-PLOR, which we developed based on FX-PLOR for EM image analysis of the helical assembly. The amplitude-weighted phase-residual was implemented as an effective potential energy. The layer-line amplitude distributions of the EM data were then scaled to the structure factors calculated from the model based on their radial amplitude profiles obtained by averaging the amplitudes within each resolution shell. The density map was calculated again, and model building and refinement were iterated.
Refinement Type
Symmetry Type
HELICAL
Map-Model Fitting and Refinement
Id
1 (1IO1)
Refinement Space
RECIPROCAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
amplitude-weighted phase residual
Overall B Value
Fitting Procedure
Details
REFINEMENT PROTOCOL--POSITIONAL AND SIMULATED ANNEALING
