7ABZ
Structure of pre-accomodated trans-translation complex on E. coli stalled ribosome.
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4YBB | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 17.4123 |
| f_angle_d | 0.6533 |
| f_chiral_restr | 0.0456 |
| f_plane_restr | 0.0059 |
| f_bond_d | 0.0028 |
| Sample |
|---|
| Structure of pre-accomodated trans-translation complex on E. coli stalled ribosome. |
| Sample Components |
| Ribosome |
| transfer-messenger RNA (tmRNA) |
| SsrA-binding protein and Elongation factor Tu 2 |
| tRNA-Phe and mRNA |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK III |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blot for 3.5 seconds before plunging |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 18452 |
| Reported Resolution (Å) | 3.21 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4YBB) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 BASE (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 35 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | -1000 |
| Maximum Defocus (nm) | -3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 0.01 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | Gctf | 1.0.6 |
| MODEL FITTING | UCSF Chimera | 1.11.2 |
| MODEL REFINEMENT | PHENIX | 1.18.2 |
| MODEL REFINEMENT | Coot | 0.9 |
| INITIAL EULER ASSIGNMENT | RELION | 3.0.8 |
| FINAL EULER ASSIGNMENT | RELION | 3.0.8 |
| CLASSIFICATION | RELION | 3.0.8 |
| RECONSTRUCTION | RELION | 3.0.8 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | 59016 | |||
