7NIC
CryoEM structure of disease related M854K MDA5-dsRNA filament in complex with ADP-AlF4(minor class)
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6GKH |
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.9203 |
f_angle_d | 0.7363 |
f_chiral_restr | 0.072 |
f_bond_d | 0.0082 |
f_plane_restr | 0.0033 |
Sample |
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Disease mutant M854K MDA5-dsRNA filament in complex with ADP-AlF4 |
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 |
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 | 62028 |
Reported Resolution (Å) | 4.3 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | HELICAL |
Axial Symmetry | C1 |
Axial Rise | 45.0795 |
Angular Rotation | 88.0297 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (6GKH) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | 147 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 29.6 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | |
Maximum Defocus (nm) | |
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 | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | RELION | |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | |
MODEL FITTING | UCSF Chimera | |
INITIAL EULER ASSIGNMENT | RELION | |
FINAL EULER ASSIGNMENT | RELION | |
CLASSIFICATION | RELION | |
RECONSTRUCTION | RELION | |
MODEL REFINEMENT | PHENIX |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 731263 |