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cryo-EM structure of ExbBD from Serratia Marcescens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YE4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.0356 f_angle_d 0.5234 f_chiral_restr 0.0349 f_plane_restr 0.0028 f_bond_d 0.0021
Sample 5-ExbB + 2-ExbD complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK II Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 158000 Reported Resolution (Å) 4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6YE4) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target correlation coefficient Overall B Value 169 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 4.58
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 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 139000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU latest CTF CORRECTION Gctf 1.06 MODEL FITTING Coot 0.8 INITIAL EULER ASSIGNMENT cryoSPARC 2.0 FINAL EULER ASSIGNMENT cryoSPARC 2.0 CLASSIFICATION cryoSPARC 2.0 RECONSTRUCTION cryoSPARC 2.0 MODEL REFINEMENT PHENIX 1.17.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 1373000 picking on 3028 images with best resolution