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The cryo-EM structure of Tick-borne encephalitis virus complexed with Fab fragment of neutralizing antibody 19/1786
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_2_deg
29.789
r_long_range_B_refined
17.505
r_long_range_B_other
17.505
r_dihedral_angle_3_deg
10.369
r_dihedral_angle_4_deg
9.29
r_dihedral_angle_1_deg
6.863
r_mcangle_it
6.387
r_mcangle_other
6.386
r_scangle_other
4.291
r_mcbond_it
3.418
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_2_deg
29.789
r_long_range_B_refined
17.505
r_long_range_B_other
17.505
r_dihedral_angle_3_deg
10.369
r_dihedral_angle_4_deg
9.29
r_dihedral_angle_1_deg
6.863
r_mcangle_it
6.387
r_mcangle_other
6.386
r_scangle_other
4.291
r_mcbond_it
3.418
r_mcbond_other
3.418
r_scbond_it
2.11
r_scbond_other
2.11
r_angle_refined_deg
1.154
r_angle_other_deg
0.879
r_chiral_restr
0.06
r_bond_refined_d
0.007
r_gen_planes_refined
0.004
r_bond_other_d
0.002
r_gen_planes_other
0.002
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 State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Wait time: 10 s
Blot time: 2 s
Blot force: -2
Drain time: 0 s
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
9797
Reported Resolution (Å)
3.9
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
I
Map-Model Fitting and Refinement
Id
1
Refinement Space
RECIPROCAL
Refinement Protocol
OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
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. ...
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.