8P8B
Mycoplasma pneumoniae large ribosomal subunit in chloramphenicol-treated cells
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 16.159 |
| f_angle_d | 0.597 |
| f_chiral_restr | 0.029 |
| f_plane_restr | 0.005 |
| f_bond_d | 0.004 |
| Sample |
|---|
| Large ribosomal subunit with some elements of the small ribosomal subunit. Focused refinement on 50S subunit of the in situ 70S subunit map. |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | CELL |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental control chamber. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SUBTOMOGRAM AVERAGING |
| Number of Particles | 30774 |
| Reported Resolution (Å) | 2.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | half maps from Warp/M |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7OOD, 7OOC) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 3.34 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3250 |
| 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 | 64000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| VOLUME SELECTION | PyTom | 0.9.7.1 |
| VOLUME SELECTION | Warp | 1.0.9 |
| IMAGE ACQUISITION | SerialEM | 3.9 |
| CTF CORRECTION | Warp | 1.0.9 |
| MODEL FITTING | Coot | 0.9.6 |
| MODEL FITTING | Coot | 0.9.8.5 |
| MODEL FITTING | CCP4 package | 8.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.0.8 |
| FINAL EULER ASSIGNMENT | Warp | 1.0.9 |
| CLASSIFICATION | RELION | 3.0.8 |
| RECONSTRUCTION | Warp | 1.0.9 |
| MODEL REFINEMENT | PHENIX | 1.20.1_4487 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF estimation and 3D CTF correction are done in Warp | |||
