6NYM

Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2d (OA-2d)


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.826
f_angle_d0.869
f_chiral_restr0.058
f_bond_d0.005
f_plane_restr0.005
Sample
Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2d (OA-2d)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles31625
Reported Resolution (Å)3.6
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD6
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolBACKBONE TRACE
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)7
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1300
Maximum Defocus (nm)2500
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 SELECTIONEMAN22.2
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTPHENIX
INITIAL EULER ASSIGNMENTRELION2.1
FINAL EULER ASSIGNMENTcryoSPARC2
CLASSIFICATIONRELION2
RECONSTRUCTIONcryoSPARC2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION540214