5O6V

The cryo-EM structure of Tick-borne encephalitis virus complexed with Fab fragment of neutralizing antibody 19/1786


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.789
r_long_range_B_refined17.505
r_long_range_B_other17.505
r_dihedral_angle_3_deg10.369
r_dihedral_angle_4_deg9.29
r_dihedral_angle_1_deg6.863
r_mcangle_it6.387
r_mcangle_other6.386
r_scangle_other4.291
r_mcbond_it3.418
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.789
r_long_range_B_refined17.505
r_long_range_B_other17.505
r_dihedral_angle_3_deg10.369
r_dihedral_angle_4_deg9.29
r_dihedral_angle_1_deg6.863
r_mcangle_it6.387
r_mcangle_other6.386
r_scangle_other4.291
r_mcbond_it3.418
r_mcbond_other3.418
r_scbond_it2.11
r_scbond_other2.11
r_angle_refined_deg1.154
r_angle_other_deg0.879
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.004
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) and Fab
Sample Components
Tick-borne encephalitis virus (strain Hypr)
Mus musculus Fab
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 Particles9797
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
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
DetailsAn initial model was generated based on the tick-borne encephalitis virus (TBEV) cryo-EM structure (PDB:5O6A) and a homology modle of the Fab 19/1786. ...An initial model was generated based on the tick-borne encephalitis virus (TBEV) cryo-EM structure (PDB:5O6A) and a homology modle of the Fab 19/1786. The model was rigid-body fitted to the electron density map of the TBEV+Fab 19/1786 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 CORRECTION