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 |
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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 |