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Closed conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Sample Closed conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
Specimen Preparation Sample Aggregation State CELL Vitrification Instrument HOMEMADE PLUNGER Cryogen Name ETHANE-PROPANE Sample Vitrification Details Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental chamber.
3D Reconstruction Reconstruction Method SUBTOMOGRAM AVERAGING Number of Particles 11557 Reported Resolution (Å) 9.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details Fitting was performed using PowerFit and Fit-in-map in ChimeraX
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 2.9
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3500 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 VOLUME SELECTION Warp 2.0.0 IMAGE ACQUISITION SerialEM CTF CORRECTION Warp 2.0.0 MODEL FITTING PowerFit MODEL FITTING UCSF ChimeraX FINAL EULER ASSIGNMENT Warp 2.0.0 CLASSIFICATION RELION 4.0.1 RECONSTRUCTION Warp 2.0.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION