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)
TypeSourceAccession CodeDetails
experimental modelPDB 3HVD 
experimental modelPDB 1J7N 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.475
f_angle_d1.287
f_chiral_restr0.07
f_bond_d0.016
f_plane_restr0.008
Sample
Fully-loaded anthrax lethal toxin in its heptameric pre-pore state
Sample Components
Protective antigen
Lethal factor
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentGATAN CRYOPLUNGE 3
Cryogen NameETHANE
Sample Vitrification Details4 uL sample was applied to grid (with 2 nm additional carbon layer) and incubated for 45 s prior blotting.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles210000
Reported Resolution (Å)3.5
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (3HVD, 1J7N)
Refinement Space
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsThe 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 TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)74.4
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO
IMAGE ACQUISITIONEPU1.10
CTF CORRECTIONSPHIRE
MODEL FITTINGiMODFIT
FINAL EULER ASSIGNMENTSPHIRE
CLASSIFICATIONSPHIRE
RECONSTRUCTIONSPHIRE
MODEL REFINEMENTPHENIX1.18.2
MODEL REFINEMENTCoot0.8.9.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION382000