7RU4
CC6.33 IgG in complex with SARS-CoV-2-6P-Mut7 S protein (RBD/Fv local refinement)
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6VXX | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 9.793 |
| f_angle_d | 1.899 |
| f_chiral_restr | 0.111 |
| f_bond_d | 0.023 |
| f_plane_restr | 0.008 |
| Sample |
|---|
| CC6.33 IgG in complex with SARS-2-CoV-6P-Mut7 S protein |
| Sample Components |
| CC6.33 IgG |
| Spike glycoprotein |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 3 s blot time |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 96012 |
| Reported Resolution (Å) | 3.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Particles were symmetry expanded and sorted on a single S protein RBD to classify only antibody-bound protomers using Relion 3.1. A mask was applied t ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6VXX) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 1500 |
| 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 | 29000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.2 |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | Gctf | 1.06 |
| MODEL FITTING | UCSF Chimera | |
| MODEL REFINEMENT | Rosetta | |
| INITIAL EULER ASSIGNMENT | RELION | 3.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3.2 |
| CLASSIFICATION | RELION | 3.1 |
| RECONSTRUCTION | cryoSPARC | 3.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
