ELECTRON MICROSCOPY

Sample

R-TYPE STRAIGHT FLAGELLAR FILAMENT

Specimen Preperation
Sample Aggregation State FILAMENT
Vitrification Instrument
Cryogen Name
Sample Vitrification Details
3D Reconstruction
Reconstruction Method HELICAL
Number of Particles 102
Reported Resolution (Å) 4.000
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, 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
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
Data Acquisition
Detector Type KODAK SO-163 FILM
Electron Dose (electrons/Å2) 20
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model JEOL 3000SFF
Minimum Defocus (nm) 1100
Maximum Defocus (nm) 2200
Minimum Tilt Angle (degrees) 0
Maximum Tilt Angle (degrees) 0
Nominal CS 1.6
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification 50000
Calibrated Magnification 47600
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
. BOTH AMPLITUDE AND PHASE