E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with A/P- and P/E-site tRNA
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7K00 | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 9.678 |
| r_dihedral_angle_6_deg | 9.507 |
| r_lrange_it | 6.646 |
| r_lrange_other | 6.646 |
| r_dihedral_angle_1_deg | 5.312 |
| r_mcangle_it | 4.653 |
| r_mcangle_other | 4.653 |
| r_scangle_it | 3.908 |
| r_scangle_other | 3.908 |
| r_dihedral_angle_2_deg | 3.207 |
| Sample |
|---|
| E. coli 70S ribosome |
| 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 | 14786 |
| Reported Resolution (Å) | 2.48 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7K00) | ||||
| Refinement Space | RECIPROCAL | ||||
| 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) | 49.88 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 300 |
| Maximum Defocus (nm) | 2000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 165000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.5.1 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | cryoSPARC | 4.5.1 |
| MODEL FITTING | UCSF ChimeraX | 1.8 |
| MODEL REFINEMENT | REFMAC | 5.8.0430 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.5.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.6.2 |
| CLASSIFICATION | cryoSPARC | 4.5.1 |
| RECONSTRUCTION | cryoSPARC | 4.6.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
