8QOI
Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNA
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6QZP | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 15.2762 |
| f_angle_d | 0.9082 |
| f_chiral_restr | 0.0519 |
| f_plane_restr | 0.0065 |
| f_bond_d | 0.0058 |
| Sample |
|---|
| Human 80S 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 | 382016 |
| Reported Resolution (Å) | 1.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6QZP) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | 38.3 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | GATAN K3 (6k x 4k) | |||||||
| Electron Dose (electrons/Å**2) | 1 | 1 | |||||||
| Imaging Experiment | 1 | 2 |
|---|---|---|
| Date of Experiment | ||
| Temperature (Kelvin) | ||
| Microscope Model | FEI TITAN KRIOS | JEOL CRYO ARM 300 |
| Minimum Defocus (nm) | 500 | 1000 |
| Maximum Defocus (nm) | 1100 | 2000 |
| Minimum Tilt Angle (degrees) | ||
| Maximum Tilt Angle (degrees) | ||
| Nominal CS | 2.7 | |
| Imaging Mode | BRIGHT FIELD | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER | |
| Nominal Magnification | ||
| Calibrated Magnification | ||
| Source | FIELD EMISSION GUN | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL REFINEMENT | PHENIX | 1.21 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
