8BIM
Initiation complex of the E. coli 70S ribosome with mRNA containing AAm6A codon in the A-site
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 15.131 |
| f_angle_d | 0.711 |
| f_chiral_restr | 0.043 |
| f_bond_d | 0.005 |
| f_plane_restr | 0.005 |
| Sample |
|---|
| Initiation complex of the E. coli 70S ribosome with mRNA containing AAm6A codon in the A-site. |
| Sample Components |
| 50S subunit |
| 30S subunit |
| 23S and 5S rRNA |
| 16S rRNA |
| mRNA and tRNA |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 670987 |
| Reported Resolution (Å) | 2.04 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | 2 | |||
| Refinement Space | REAL | REAL | |||
| Refinement Protocol | RIGID BODY FIT | FLEXIBLE FIT | |||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Following rigid body fitting we used online Namdiantor tool to perform initial flexible fitting: https://namdinator.au.dk/namdinator/ | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 900 |
| Maximum Defocus (nm) | 2100 |
| 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 | |
| Calibrated Magnification | 105000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.3.0 |
| IMAGE ACQUISITION | EPU | 2.1 |
| CTF CORRECTION | cryoSPARC | 3.3.0 |
| MODEL FITTING | UCSF ChimeraX | 1.2.5 |
| MODEL REFINEMENT | PHENIX | Online |
| MODEL FITTING | ISOLDE | 1.4 |
| MODEL REFINEMENT | PHENIX | 1.19.2-4158 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.3.0 |
| CLASSIFICATION | cryoSPARC | 3.3.0 |
| RECONSTRUCTION | cryoSPARC | 3.3.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 500 | |||
