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Cryo-EM structure of the A946T MDA5-dsRNA filament
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9F0J
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.678 f_angle_d 0.536 f_chiral_restr 0.039 f_plane_restr 0.004 f_bond_d 0.003
Sample Mouse MDA5 A946T in complex with double stranded RNA Sample Components Mouse MDA5 A946T double stranded RNA
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 2-4 s blotting, 15 s wait time
3D Reconstruction Reconstruction Method HELICAL Number of Particles 234719 Reported Resolution (Å) 3.97 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 44.58 Angular Rotation 89.44
Map-Model Fitting and Refinement Id 1 (9F0J) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation coefficient Overall B Value 90 Fitting Procedure Details Initial local fitting with Fit-in-Map in Chimera followed by real space refinement in Phenix.
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 44
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 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 96000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO IMAGE ACQUISITION SerialEM 3 CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT RELION 4.0 FINAL EULER ASSIGNMENT RELION 4.0 CLASSIFICATION RELION 4.0 RECONSTRUCTION RELION 4.0 MODEL REFINEMENT PHENIX 1.21
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1378603