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The cryo-EM structure of BamACDE complex from Neisseria gonorrhoeae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K3B experimental model PDB 5WAQ experimental model PDB 5WAM
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.103 f_angle_d 0.545 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.002
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot force of 2, blot time of 15 seconds.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 95431 Reported Resolution (Å) 4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (4K3B, 5WAQ, 5WAM) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 41.87
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 2230 Maximum Defocus (nm) 9700 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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.2 IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC 3.2 MODEL FITTING UCSF ChimeraX CLASSIFICATION cryoSPARC 3.2 RECONSTRUCTION cryoSPARC 3.2 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4552267