6ZXL

Fully-loaded anthrax lethal toxin in its heptameric pre-pore state and PA7LF(2+1A) arrangement


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZXK 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.395
f_angle_d1.345
f_chiral_restr0.066
f_bond_d0.013
f_plane_restr0.008
Sample
Fully-loaded anthrax lethal toxin in its heptameric pre-pore state and PA7LF(2+1A) arrangement
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 Particles44000
Reported Resolution (Å)4.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6ZXK)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
DetailsThe previously generated PA7LF(2+1B) model (PDB:6ZXK) served as starting point and was placed into the density using rigid-body fit in Chimera. From t ...The previously generated PA7LF(2+1B) model (PDB:6ZXK) served as starting point and was placed into the density using rigid-body fit in Chimera. From this model, chain J was fitted into the density corresponding to the third LF, located adjacent to the second LF. For the entire model a restrained refinement in phenix was performed. The resulting model was further refined with a combination of phenix and coot. Unresolved regions were deleted and side chain information was removed for less well-resolved 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
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