Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex (pICln PBM local refinement)
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6V0O | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.8235 |
| f_angle_d | 0.5195 |
| f_chiral_restr | 0.0423 |
| f_plane_restr | 0.0034 |
| f_bond_d | 0.0032 |
| Sample |
|---|
| PRMT5/WDR77 in complex with 6S (PBM local refinement) |
| Sample Components |
| PRMT5/WDR77 |
| 6S complex |
| Methylosome subunit pICln |
| small nuclear ribonucleoproteins Sm D1, E, F, G |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 285661 |
| Reported Resolution (Å) | 3.36 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6V0O, 6V0O, 6V0O) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | real space correlation | ||||
| Overall B Value | 98.6 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 53.112 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS TALOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2200 |
| 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 | 36000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Topaz | |
| IMAGE ACQUISITION | SerialEM | 4.1 |
| CTF CORRECTION | cryoSPARC | 4.4.1 |
| MODEL FITTING | UCSF ChimeraX | |
| MODEL FITTING | ISOLDE | |
| CLASSIFICATION | cryoSPARC | 4.41 |
| RECONSTRUCTION | cryoSPARC | 4.4.1 |
| MODEL REFINEMENT | PHENIX | 1.21.1_5286 |
| 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 | as implemented in cryosparc live | 2100293 | topaz | |
