ELECTRON MICROSCOPY

Sample

Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells

Specimen Preperation
Sample Aggregation State CELL
Vitrification Instrument ?
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SUBTOMOGRAM AVERAGING
Number of Particles 1001
Reported Resolution (Å) 17
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space ?
Refinement Protocol RIGID BODY FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details Initial fitting with PowerFit into the map of the closed conformation of the complex (EMD-54986). The closed conformation (PDB: 9SLC) was rigid body fitted into the open conformation of the map, and the AlphaFold3 multimer prediction of subcomplex SecYEG-DF was aligned to and replaced the old AlphaFold2 models of these proteins. The SecYEG-DF subcomplex as well as the remaining proteins were each rigid body fitted as single rigid bodies using ChimeraX fit-to-map.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 2.9
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 1500
Maximum Defocus (nm) 3500
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
VOLUME SELECTION Warp 1.0.9
CTF CORRECTION Warp 1.0.9
MODEL FITTING PowerFit ?
MODEL FITTING UCSF ChimeraX ?
FINAL EULER ASSIGNMENT RELION 4.0.1
RECONSTRUCTION RELION 4.0.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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