7YYM
Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substrate
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 13.029 |
| f_angle_d | 0.794 |
| f_chiral_restr | 0.046 |
| f_plane_restr | 0.011 |
| f_bond_d | 0.004 |
| Sample |
|---|
| Pre-dicing state of mouse somatic dicer with pre-mir-15a |
| Sample Components |
| Pre-dicing state of mouse somatic dicer |
| pre-mir-15a |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Described in STAR methods |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 154665 |
| Reported Resolution (Å) | 4.19 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | 2 | 3 | ||
| Refinement Space | REAL | REAL | REAL | ||
| Refinement Protocol | FLEXIBLE FIT | FLEXIBLE FIT | FLEXIBLE FIT | ||
| Refinement Target | Ramachandran Plot, Rotamer Analysis, Density Analysis | Correlation coefficient | Ramachandran Plot, Rotamer Analysis, Clash Score | ||
| Overall B Value | 134.8 | 134.8 | 134.8 | ||
| Fitting Procedure | |||||
| Details | Endoribonuclease mouse Dicer from AlphaFold database was used as initial model. Initial local fitting was done using Chimera and then Coot's Real Spac ... | PHENIX Real-space refinement was used for flexible fitting. | ISOLDE was used for flexible fitting with torsion restraints defined for polypeptide and distance restraints for polyribonucleotide chain. | ||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 55 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3500 |
| 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 |
| CTF CORRECTION | cryoSPARC | v3.3.1 |
| MODEL FITTING | UCSF Chimera | 1.15 |
| CLASSIFICATION | cryoSPARC | v3.3.1 |
| RECONSTRUCTION | cryoSPARC | v3.3.1 |
| MODEL REFINEMENT | Coot | 0.9.6 |
| MODEL REFINEMENT | PHENIX | 1.19.2-4158 |
| MODEL REFINEMENT | ISOLDE | 1.1.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1212966 | |||
