8R8K
XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8CIM |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 3.589 |
f_angle_d | 0.461 |
f_chiral_restr | 0.042 |
f_plane_restr | 0.004 |
f_bond_d | 0.003 |
Sample |
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XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein |
Sample Components |
XBB-4 Fab |
BA.2.12.1 Spike Glycoprotein Ectodomain |
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 | 61333 |
Reported Resolution (Å) | 3.41 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Determined by cryoSPARC. Local refinement job centred around one fab and RBD. |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (8CIM) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON IV (4k 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) | 2700 |
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 | |
Calibrated Magnification | 165000 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | cryoSPARC | |
MODEL FITTING | Coot | |
MODEL REFINEMENT | PHENIX | |
INITIAL EULER ASSIGNMENT | cryoSPARC | |
FINAL EULER ASSIGNMENT | cryoSPARC | |
CLASSIFICATION | cryoSPARC | |
RECONSTRUCTION | cryoSPARC |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | Patch CTF and Motion correction, on-the-fly. | 3282771 | Blob picker in cryoSPARC live interface. |