7ZPK
Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substrate and TARBP2 subunit
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7ZPJ | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 13.019 |
| f_angle_d | 0.848 |
| f_chiral_restr | 0.053 |
| f_plane_restr | 0.015 |
| f_bond_d | 0.004 |
| Sample |
|---|
| Pre-dicing state of mouse somatic dicer with pre-mir-15a and TARBP2 |
| Sample Components |
| Pre-dicing state of mouse somatic dicer with TARBP2 |
| 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 | 437518 |
| Reported Resolution (Å) | 3.81 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7ZPJ, 7ZPJ, 7ZPJ) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | 189.2 | ||||
| Fitting Procedure | |||||
| Details | Initial model used from PDB ID:7ZPJ TARBP2 dsRBD domain 1: initial model from PDB ID:7ZPJ TARBP2 dsRBD domains 2,3: manually fitted into EM map accor ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 60.198 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| 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 | ISOLDE | 1.1.0 |
| MODEL REFINEMENT | PHENIX | 1.19.2-4158 |
| MODEL REFINEMENT | Coot | 0.9.6 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2219694 | |||
