5U4J
Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 41.526 |
| r_dihedral_angle_3_deg | 15.794 |
| r_long_range_B_refined | 9.293 |
| r_dihedral_angle_4_deg | 8.729 |
| r_mcangle_it | 4.149 |
| r_dihedral_angle_1_deg | 3.852 |
| r_mcbond_it | 2.195 |
| r_scbond_it | 1.286 |
| r_angle_refined_deg | 0.904 |
| r_chiral_restr | 0.066 |
| Sample |
|---|
| Non-stop ribosomal complex with ArfA and RF2 |
| Sample Components |
| 30S subunit |
| 50S subunit |
| Alternative ribosome-rescue factor A |
| Peptide chain release factor 2 |
| P-site tRNA fMet |
| mRNA |
| 23S rRNA |
| 16S rRNA |
| 30S ribosomal protein S3 |
| 30S ribosomal protein S4 |
| 30S ribosomal protein S5 |
| 30S ribosomal protein S12 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Grids were blotted for 3.5 s |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 155440 |
| Reported Resolution (Å) | 3.7 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Average FSC | ||||
| Overall B Value | 108.501 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 20 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | JEOL 3200FSC |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | 83822 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 1.4 |
| CTF CORRECTION | CTFFIND | 4 |
| MODEL FITTING | UCSF Chimera | |
| INITIAL EULER ASSIGNMENT | RELION | 2.0 |
| FINAL EULER ASSIGNMENT | RELION | 2.0 |
| RECONSTRUCTION | RELION | 2.0 |
| MODEL REFINEMENT | REFMAC | 5.8 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
