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Cryo-EM structure of the Agrobacterium T-pilus
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.129 f_angle_d 0.572 f_chiral_restr 0.034 f_bond_d 0.003 f_plane_restr 0.003
Sample T-pilus Sample Components VirB2 Phosphatidylglycerol 16:1/18:1
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 3543 Reported Resolution (Å) 3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C5 Axial Rise 13.44 Angular Rotation 32.62 Axial Symmetry C1 Axial Rise 13.44 Angular Rotation 32.62 Axial Symmetry C1 Axial Rise 13.44 Angular Rotation 32.62
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 4.0beta2 IMAGE ACQUISITION SerialEM 3-9-0beta7 CTF CORRECTION RELION 4.0beta2 MODEL FITTING Rosetta 3 MODEL REFINEMENT PHENIX 1.19.2 INITIAL EULER ASSIGNMENT RELION 4.0beta2 FINAL EULER ASSIGNMENT RELION 4.0beta2 CLASSIFICATION RELION 4.0beta2 RECONSTRUCTION RELION 4.0beta2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 10934 Filaments were manually picked using EMAN2 e2helixboxer and particles were extracted by RELION.