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Structure of a glycosylated Vibrio alginolyticus lateral flagellar filament
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.105 f_angle_d 0.614 f_chiral_restr 0.037 f_bond_d 0.004 f_plane_restr 0.003
Sample Structure of a glycosylated Vibrio alginolyticus lateral flagellar filament
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 566405 Reported Resolution (Å) 2.37 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 4.728 Angular Rotation 65.351
Map-Model Fitting and Refinement Id 1 2 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 80
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 Minimum Defocus (nm) 500 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model JEOL CRYOSPECPORTER Nominal Magnification 60000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.5.3 IMAGE ACQUISITION SerialEM 4.1.6 CTF CORRECTION cryoSPARC 4.5.3 MODEL FITTING UCSF ChimeraX 1.11.1 MODEL REFINEMENT PHENIX 1.20.1_4487: MODEL REFINEMENT Coot 0.9.8.95 MODEL REFINEMENT PHENIX 1.20.1_4487: CLASSIFICATION cryoSPARC 4.5.3 RECONSTRUCTION cryoSPARC 4.5.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2905795