7X96
The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab847
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5CCK |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.1853 |
f_angle_d | 0.4913 |
f_chiral_restr | 0.0407 |
f_plane_restr | 0.0048 |
f_bond_d | 0.0024 |
Sample |
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The SARS-CoV-2 spike protein bound with the Fab fragment of a human neutralizing antibody Ab847 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 249414 |
Reported Resolution (Å) | 3.4 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
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Id | 1 (5CCK) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | AB INITIO MODEL | ||||
Refinement Target | Corelation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 2400 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 105000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | crYOLO | |
IMAGE ACQUISITION | EPU | 2.9 |
CTF CORRECTION | CTFFIND | 4 |
MODEL FITTING | Coot | 0.9.6 |
MODEL REFINEMENT | PHENIX | 1.19.2-4158 |
INITIAL EULER ASSIGNMENT | RELION | 3.1.2 |
FINAL EULER ASSIGNMENT | RELION | 3.1.2 |
CLASSIFICATION | RELION | 3.1.2 |
RECONSTRUCTION | RELION | 3.1.2 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |