Experiment: 6V11

Lon Protease from Yersinia pestis

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ON2

Sample
Lon Protease from Yersinia pestis

Specimen Preparation
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 nitro ...	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	140506
Reported Resolution (Å)	3.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (6ON2)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Correlation coefficient
Overall B Value	115
Fitting Procedure
Details	Initial rigid body docking was done using UCSF Chimera

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (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.

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	Leginon	3.0
CTF CORRECTION	Warp	1.0.7
MODEL FITTING	Coot	0.8.8
INITIAL EULER ASSIGNMENT	cryoSPARC	2.11.0
FINAL EULER ASSIGNMENT	cryoSPARC	2.11.0
CLASSIFICATION	cryoSPARC	2.11.0
RECONSTRUCTION	cryoSPARC	2.11.0
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 Warp	412719	Particles were selected from a subset of micrographs using BoxNet automated particle picker