6ZXJ

Fully-loaded anthrax lethal toxin in its heptameric pre-pore state, in which the third lethal factor is masked out (PA7LF3-masked)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HVD
experimental model	PDB	1J7N

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.475
f_angle_d	1.287
f_chiral_restr	0.07
f_bond_d	0.016
f_plane_restr	0.008

Sample
Fully-loaded anthrax lethal toxin in its heptameric pre-pore state
Sample Components
Protective antigen
Lethal factor

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	GATAN CRYOPLUNGE 3
Cryogen Name	ETHANE
Sample Vitrification Details	4 uL sample was applied to grid (with 2 nm additional carbon layer) and incubated for 45 s prior blotting.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	210000
Reported Resolution (Å)	3.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3HVD, 1J7N)
Refinement Space
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	The protective antigen (PA) monomer from 3HVD was placed seven times into the density corresponding to the heptameric PA ring using the rigid-body fit ...	The protective antigen (PA) monomer from 3HVD was placed seven times into the density corresponding to the heptameric PA ring using the rigid-body fit in Chimera. Two copies of the monomeric lethal factor (LF) from 1J7N were fitted similarly into the corresponding LF density located atop of the PA7 ring. The resulting model was then flexibly fitted using iMODFIT. The model was further refined in iterative rounds of phenix and coot. Unresolved regions were deleted and side chain information was removed for less well-defined regions.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	74.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
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	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO
IMAGE ACQUISITION	EPU	1.10
CTF CORRECTION	SPHIRE
MODEL FITTING	iMODFIT
FINAL EULER ASSIGNMENT	SPHIRE
CLASSIFICATION	SPHIRE
RECONSTRUCTION	SPHIRE
MODEL REFINEMENT	PHENIX	1.18.2
MODEL REFINEMENT	Coot	0.8.9.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		382000

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 R01GM157729.