CryoEM structure of the MDA5-dsRNA filament with 93 degree twist and without nucleotide
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6G1X | |
| Sample |
|---|
| MDA5-dsRNA helical filament without nucleotide |
| Sample Components |
| MDA5 (IFIH1) |
| Double-stranded RNA from bacteriophage Phi6, generated by n vitro translation |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 19111 |
| Reported Resolution (Å) | 4.16 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 44.366 |
| Angular Rotation | 93.0596 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6G1X) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 175 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 27 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | -1800 |
| Maximum Defocus (nm) | -2700 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | 75000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 2.1.0 |
| IMAGE ACQUISITION | EPU | 1.9.1 |
| CTF CORRECTION | Gctf | 1.06 |
| MODEL FITTING | Coot | 0.8.9 |
| INITIAL EULER ASSIGNMENT | RELION | 2.1.0 |
| FINAL EULER ASSIGNMENT | RELION | 2.1.0 |
| CLASSIFICATION | RELION | 2.1.0 |
| RECONSTRUCTION | RELION | 2.1.0 |
| MODEL REFINEMENT | PHENIX | 1.14 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 137601 | |||
