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2.5 A cryo-EM structure of the in vitro FimD-catalyzed assembly of type 1 pilus rod
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OH0
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.1568 f_angle_d 0.4384 f_chiral_restr 0.0408 f_plane_restr 0.0028 f_bond_d 0.0025
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 ul sample, 30 s wait time, 0.5 s drain time, 6 s blotting
3D Reconstruction Reconstruction Method HELICAL Number of Particles 135000 Reported Resolution (Å) 2.52 Resolution Method FSC 0.143 CUT-OFF Other Details standard Relion protocol Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 7.8 Angular Rotation 115
Map-Model Fitting and Refinement Id 1 (5OH0) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value 46.49 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 49
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification 47393 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.06 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT RELION 3.08 FINAL EULER ASSIGNMENT RELION 3.08 CLASSIFICATION RELION 3.08 RECONSTRUCTION RELION 3.08 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 416000 Autopicking based on the 2D classes from manually chosen filaments