Staphylococcus aureus 70S ribosome with p/E tRNA and RRF oriented towards the LSU (postTC-RRF-LSU)
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 9GHG | |
| in silico model | AlphaFold | ||
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_dihedral_angle_6_deg | 9.1106 |
| s_dihedral_angle_3_deg | 8.6642 |
| s_dihedral_angle_1_deg | 4.5561 |
| s_dihedral_angle_2_deg | 1.8253 |
| s_angle_nonh_deg | 0.7894 |
| s_nbtor | 0.1837 |
| s_nbd | 0.1814 |
| s_hbond_nbd | 0.1316 |
| s_chiral_restr | 0.0252 |
| s_bond_nonh_d | 0.0024 |
| Sample |
|---|
| S. aureus 70S ribosome in complex with a tRNA and ribosome recycling factor (RRF) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 25462 |
| Reported Resolution (Å) | 2.62 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (9GHG) | ||||
| Refinement Space | |||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 30 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 1000 |
| 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 | 4.7.1-cuda12+250814 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | cryoSPARC | 4.7.1-cuda12+250814 |
| MODEL FITTING | Coot | 0.9.8.96 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.7.1-cuda12+250814 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.7.1-cuda12+250814 |
| CLASSIFICATION | cryoSPARC | 4.7.1-cuda12+250814 |
| RECONSTRUCTION | cryoSPARC | 4.7.1-cuda12+250814 |
| MODEL REFINEMENT | Coot | 0.9.8.96 |
| MODEL REFINEMENT | Servalcat | 0.4.105 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2556350 | |||
