7OOD
Mycoplasma pneumoniae 50S subunit of ribosomes in chloramphenicol-treated cells
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 18.578 |
| f_angle_d | 1.3495 |
| f_chiral_restr | 0.1058 |
| f_bond_d | 0.0105 |
| f_plane_restr | 0.0092 |
| Sample |
|---|
| cryo-electron tomograms of chloramphenicol-treated Mycoplasma pneumoniae cells |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | CELL |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | ack-side blotting for 2-3 second before plunging using a manual plunger without an environmental chamber |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SUBTOMOGRAM AVERAGING |
| Number of Particles | 17890 |
| Reported Resolution (Å) | 3.4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Map generated by focused refinement on the 50S subunit in M |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3J9W, 1DIV, 1ZAV, 4YBB, 4YBB) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 3.2 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 3750 |
| 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 | 81000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL REFINEMENT | Coot | 0.9 |
| MODEL REFINEMENT | PHENIX | 1.18 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
