8QPR
SARS-CoV-2 S protein bound to human neutralising antibody UZGENT_G5
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7K8V |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.01 |
f_angle_d | 0.812 |
f_chiral_restr | 0.053 |
f_bond_d | 0.006 |
f_plane_restr | 0.006 |
Sample |
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Complex of SARS-CoV2 S Protein (Wuhan) and FAB fragment of neutralising human antibody UZGENT_G5 |
Sample Components |
SARS-CoV2 S Protein with Fibritin (trimerization) tag |
FAB fragment of neutralising human antibody UZGENT_G5 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | GATAN CRYOPLUNGE 3 |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 161643 |
Reported Resolution (Å) | 3.8 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (7K8V) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | 60 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 60 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | JEOL CRYO ARM 300 |
Minimum Defocus (nm) | 600 |
Maximum Defocus (nm) | 2500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | 60000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | |
CTF CORRECTION | cryoSPARC | |
MODEL FITTING | Coot | 0.9.5 |
INITIAL EULER ASSIGNMENT | cryoSPARC | |
FINAL EULER ASSIGNMENT | cryoSPARC | |
CLASSIFICATION | cryoSPARC | |
RECONSTRUCTION | cryoSPARC | |
MODEL REFINEMENT | PHENIX | 1.18.2_3874: |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING ONLY | 226273 |