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Cryo-EM structure of the I923V MDA5-dsRNA filament in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BKQ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.998 f_angle_d 0.56 f_chiral_restr 0.041 f_bond_d 0.003 f_plane_restr 0.003
Sample Mouse MDA5 I923V in complex with double stranded RNA Sample Components Mouse MDA5 I923V 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 337327 Reported Resolution (Å) 4.21 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 43.92 Angular Rotation 84.15
Map-Model Fitting and Refinement Id 1 (7BKQ) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation coefficient Overall B Value 130 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO IMAGE ACQUISITION EPU 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 683122