Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 54
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 9OV3 | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 25.178 |
| f_angle_d | 0.564 |
| f_chiral_restr | 0.029 |
| f_plane_restr | 0.004 |
| f_bond_d | 0.003 |
| Sample |
|---|
| ribonuclease P RNA |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Grids were glow-discharged on both sides prior to vitrification. Vitrification was performed using a Vitrobot Mark IV with a 10s wait time, followed b ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 45331 |
| Reported Resolution (Å) | 3.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (9OV3) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | maximization of map-to-model correlation | ||||
| Overall B Value | 57 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 53 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 2000 |
| 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 | 165000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | The alignment procedure was performed using the EPU software utilizing its autofocus and auto-tuning functions for initial microscope alignment. This was followed by manual fine-tuning adjustments of the beam shift, stigmation, and focus controls to ensure optimal image quality. Grid squares were screened systematically, ensuring the selection of areas with appropriate ice thickness and particle distribution. Image shift calibration and eucentric height adjustment were performed within EPU to maintain beam alignment during data acquisition |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.6 |
| IMAGE ACQUISITION | EPU | 3.1 |
| CTF CORRECTION | cryoSPARC | 4.6 |
| MODEL FITTING | UCSF ChimeraX | 1.9 |
| MODEL FITTING | Coot | 0.9.8.95 |
| MODEL REFINEMENT | PHENIX | 1.21.2_5419 |
| CLASSIFICATION | cryoSPARC | 4.6 |
| RECONSTRUCTION | cryoSPARC | 4.6 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF correction was performed in cryoSPARC by patch-based motion correction followed by patch-based CTF estimation, providing per-particle local CTF parameters that were applied during 3D refinement for phase and amplitude correction of all particles | 21475910 | An iterative particle-cleaning workflow was applied, combining 2D classification and heterogeneous refinement with decoy classes to achieve exhaustive particle selection. | |
