5O6V | pdb_00005o6v

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

ELECTRON MICROSCOPY

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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
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. 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 Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	22

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	75000
Calibrated Magnification	75000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	EMAN	2.1
IMAGE ACQUISITION	EPU	2
CTF CORRECTION	Gctf	1.06
MODEL FITTING	UCSF Chimera	1.11
MODEL FITTING	Coot	0.8.7
MODEL REFINEMENT	PHENIX	1.11
MODEL REFINEMENT	REFMAC	5.8.0158
INITIAL EULER ASSIGNMENT	RELION	1.4
FINAL EULER ASSIGNMENT	RELION	1.4
CLASSIFICATION	RELION	1.4
RECONSTRUCTION	RELION	1.4

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		12098