6ON2

Lon Protease from Yersinia pestis with Y2853 substrate

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.144
f_angle_d	0.92
f_chiral_restr	0.059
f_plane_restr	0.008
f_bond_d	0.007

Sample
Lon protease bound to Y2853 substrate

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	118143
Reported Resolution (Å)	3
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 ...	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
Point Symmetry	C1

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/Å**2)	52

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
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	1176206	template-based cross correlation with FindEM

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.