7PJS
Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C)
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 15.2597 |
| f_angle_d | 0.6322 |
| f_chiral_restr | 0.0387 |
| f_plane_restr | 0.0049 |
| f_bond_d | 0.0048 |
| Sample |
|---|
| E. coli ribosome complex 70S-Apr-EF-G-GDP-Pi-fMet-Phe-tRNAPhe-tRNA-fMet-mRNA |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Manual blotting & plunge-freezing |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 537761 |
| Reported Resolution (Å) | 2.35 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6YSS, 4AQY, 5LZD) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | RSCC | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Instead of Chimera ChimeraX was used. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 30 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 200 |
| Maximum Defocus (nm) | 1500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 0.01 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 59000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Aberration corrections performed using Cs image corrector (CEOS company) |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Gautomatch | |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | Coot | 0.9.3 |
| MODEL FITTING | UCSF Chimera | 1.2 |
| MODEL FITTING | ISOLDE | 1.1.0 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1 |
| FINAL EULER ASSIGNMENT | RELION | 3.1 |
| CLASSIFICATION | RELION | 3.1 |
| RECONSTRUCTION | RELION | 3.1 |
| MODEL REFINEMENT | PHENIX | 16 |
| MODEL REFINEMENT | ISOLDE | 1.1.0 |
| MODEL REFINEMENT | Coot | 0.9.3 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1326729 | |||
