5O6V
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 |
Sample |
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Tick-borne encephalitis virus (strain HYPR) and Fab |
Sample Components |
Tick-borne encephalitis virus (strain Hypr) |
Mus musculus Fab |
Specimen Preparation | |
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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 | |
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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. ... |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON II (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 22 |
Imaging Experiment | 1 |
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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 | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 12098 |