ELECTRON MICROSCOPY

Sample

Lon protease bound to Y2853 substrate

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details 4 uL of sample was applied per grid and manually blotted for 4 seconds followed by immediately plunge-freezing in liquid ethane cooled by liquid nitrogen.
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 118143
Reported Resolution (Å) 3.0
Resolution Method FSC 0.143 CUT-OFF
Other Details Focused classification of final reconstruction was performed on E and F "step" subunits, resulting in a reconstruction with an overall resolution of 3.5 A by FSC 0.143. The two maps were stitched together using vop max in UCSF Chimera. All three maps (two original and final composite) are deposited in this entry.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol AB INITIO MODEL
Refinement Target Correlation coefficient
Overall B Value 52
Fitting Procedure ?
Details Initial homology model was built using SWISS-MODEL and initial rigid body docking was done using UCSF Chimera
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 52.0
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TALOS ARCTICA
Minimum Defocus (nm) 800
Maximum Defocus (nm) 1200
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 36000
Calibrated Magnification 43478
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details Coma-free alignment procedure from Herzik & Wu, Nature Methods (2017). Preliminary grid screening was performed manually prior to data collection.
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION FindEM 1
IMAGE ACQUISITION Leginon 3.0
CTF CORRECTION RELION 2.0b
MODEL FITTING Coot 0.8.8
INITIAL EULER ASSIGNMENT RELION 2.0b
FINAL EULER ASSIGNMENT RELION 2.0b
CLASSIFICATION RELION 2.0b
RECONSTRUCTION RELION 2.0b
MODEL REFINEMENT PHENIX 1.11.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING ONLY CTF correction in RELION
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