9GCH
Human mitochondrial RNase Z with tRNA-His-CCA, SDR5C1/TRMT10C focus
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7ONU | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 12.452 |
| r_long_range_B_refined | 11.829 |
| r_long_range_B_other | 11.829 |
| r_scangle_other | 5.615 |
| r_dihedral_angle_1_deg | 4.722 |
| r_mcangle_it | 3.442 |
| r_mcangle_other | 3.442 |
| r_scbond_it | 3.195 |
| r_scbond_other | 3.195 |
| r_dihedral_angle_2_deg | 3.184 |
| Sample |
|---|
| RNAseZ with mt-tRNA-His |
| Sample Components |
| RNAseZ |
| mt-tRNA-His |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 293773 |
| Reported Resolution (?) | 1.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7ONU) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/?**2) | 48 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 400 |
| Maximum Defocus (nm) | 2000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Warp | 1.0.9 |
| CTF CORRECTION | Warp | 1.0.9 |
| MODEL FITTING | Coot | 0.9.8 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.3.1 |
| FINAL EULER ASSIGNMENT | RELION | 5.0-beta-1 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 4773315 | |||
