8QRH

Inactivated tick-borne encephalitis virus (TBEV) vaccine strain Sofjin-Chumakov


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5O6A 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.1831
f_angle_d0.7227
f_chiral_restr0.0455
f_plane_restr0.0084
f_bond_d0.0026
Sample
Tick-borne encephalitis virus (STRAIN Sofjin-Chumakov)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles70491
Reported Resolution (Å)3.6
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsThe local non-uniform refinement was used on the set of particles subjected to I symmetry expansion
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (5O6A)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)68
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.0
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTCoot
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION