7BKP
CryoEM structure of disease related M854K MDA5-dsRNA filament in complex with ATP
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6G19 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.021 |
f_angle_d | 0.7543 |
f_chiral_restr | 0.0483 |
f_bond_d | 0.0092 |
f_plane_restr | 0.0038 |
Sample |
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M854K MDA5-dsRNA filament in complex with ATP |
Sample Components |
INTERFERON-INDUCED HELICASE C DOMAIN-CONTAINING PROTEIN |
RNA |
Specimen Preparation | |
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Sample Aggregation State | FILAMENT |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE-PROPANE |
Sample Vitrification Details | Grids were blotted for 3 s; blot force 10, 5, 0, -5, -10 |
3D Reconstruction | |
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Reconstruction Method | HELICAL |
Number of Particles | 383128 |
Reported Resolution (Å) | 2.8 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | HELICAL |
Axial Symmetry | C1 |
Axial Rise | 43.92 |
Angular Rotation | 74.63 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (6G19) | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | OTHER | ||||
Refinement Target | Correlation coefficient | ||||
Overall B Value | 50 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | -1200 |
Maximum Defocus (nm) | -2500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | DARK FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | RELION | 3.1 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | |
MODEL FITTING | UCSF Chimera | 1.13.1 |
MODEL REFINEMENT | PHENIX | 1.18.2 |
INITIAL EULER ASSIGNMENT | RELION | 3.1 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
CLASSIFICATION | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 1068108 |