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Cryo-EM Structure of OmpC3-MlaA-MlaC Complex in MSP2N2 Nanodiscs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NUP experimental model PDB 5UWA
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.242 f_angle_d 1.174 f_chiral_restr 0.069 f_bond_d 0.007 f_plane_restr 0.007
Sample OmpC3-MlaA complex in MSP2N2 nanodiscs disulfide-bonded to MlaC Sample Components Outer membrane porin C Complex of MlaA disulfide trapped with MlaC
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 76463 Reported Resolution (Å) 3.25 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5NUP, 5NUP, 5NUP, 5NUP, 5UWA) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation coefficient Overall B Value 69.1 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 90
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2000 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.0.0 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 4.0.0 MODEL FITTING UCSF Chimera 1.15 INITIAL EULER ASSIGNMENT cryoSPARC 4.0.0 FINAL EULER ASSIGNMENT cryoSPARC 4.0.0 CLASSIFICATION cryoSPARC 4.0.0 RECONSTRUCTION cryoSPARC 4.0.0 MODEL REFINEMENT Coot 0.9.4.1 EL MODEL REFINEMENT PHENIX 1.20.1-4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF routine in cryoSPARC 2434319 We performed automated particle picking using Blob and Template Picker for initial template picking and final sampling respectively.