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 5O6A | pdb_00005o6a

The cryo-EM structure of Tick-borne encephalitis virus mature particle


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2SVB 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.111
r_dihedral_angle_3_deg9.194
r_long_range_B_refined8.62
r_long_range_B_other8.62
r_dihedral_angle_4_deg7.879
r_dihedral_angle_1_deg6.542
r_mcangle_it2.822
r_mcangle_other2.822
r_scangle_other1.706
r_mcbond_it1.491
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.111
r_dihedral_angle_3_deg9.194
r_long_range_B_refined8.62
r_long_range_B_other8.62
r_dihedral_angle_4_deg7.879
r_dihedral_angle_1_deg6.542
r_mcangle_it2.822
r_mcangle_other2.822
r_scangle_other1.706
r_mcbond_it1.491
r_mcbond_other1.491
r_angle_refined_deg1.057
r_angle_other_deg0.851
r_scbond_it0.807
r_scbond_other0.806
r_chiral_restr0.056
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Tick-borne encephalitis virus (strain HYPR)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsWait time: 10 s Blot time: 2 s Blot force: -2 Drain time: 0 s
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles11882
Reported Resolution (Å)3.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (2SVB)
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
DetailsAn initial model was generated based on the known crystal structure of the ecto-domain (PDB:1SVB), Dengue virus type 2 and the Zika virus (PDB:5IRE,3J ...An initial model was generated based on the known crystal structure of the ecto-domain (PDB:1SVB), Dengue virus type 2 and the Zika virus (PDB:5IRE,3J27) using the program Modeller. The model was rigid-body fitted to the electron density map of the TBEV particle using the program Chimera. Subsequently, the structure was manually corrected using the program Coot, followed by real-space refinement in Phenix and reciprocal space refinement in Refmac5.
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)22
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification75000
Calibrated Magnification75000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONEMAN2.1
IMAGE ACQUISITIONEPU2
CTF CORRECTIONGctf1.06
MODEL FITTINGUCSF Chimera1.11
MODEL FITTINGCoot0.8.7
MODEL REFINEMENTPHENIX1.11
MODEL REFINEMENTREFMAC5.8.0158
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
CLASSIFICATIONRELION1.4
RECONSTRUCTIONRELION1.4
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION19111