9F9Y
SARS-CoV-2 BA-2.87.1 Spike ectodomain
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8R1C |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 9.937 |
f_angle_d | 0.453 |
f_chiral_restr | 0.042 |
f_bond_d | 0.003 |
f_plane_restr | 0.003 |
Sample |
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BA-2.87.1 variant SARS-CoV2 S protein |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 37441 |
Reported Resolution (Å) | 2.8 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Determined in cryosparc local resolution estimation module. |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C3 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (8R1C) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | OTHER | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | Phenix real space refinement with manual checks using coot. |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 2600 |
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 | 165000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | v.4.3.1 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | cryoSPARC | v.4.3.1 |
MODEL FITTING | Coot | |
MODEL FITTING | PHENIX | |
INITIAL EULER ASSIGNMENT | cryoSPARC | |
FINAL EULER ASSIGNMENT | cryoSPARC | v.4.3.1 |
CLASSIFICATION | cryoSPARC | v.4.3.1 |
RECONSTRUCTION | cryoSPARC | v.4.3.1 |
MODEL REFINEMENT | PHENIX | |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | Determined using cryoSPARC live patch CTF correction. | 504319 |