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Cryo-EM structure of lipid-bound human myoferlin (25 mol% DOPS/5 mol% PI(4,5)P2 nanodisc)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.6588 f_angle_d 0.7902 f_chiral_restr 0.0498 f_plane_restr 0.0069 f_bond_d 0.0036
Sample Soluble human myoferlin (residues 1-1997) bound to an MSP2N2-based lipid nanodisc (comprising 25 mol% DOPS and 5 mol% PI(4,5)P2)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 233637 Reported Resolution (Å) 2.56 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value 152.37 Fitting Procedure Details Iterative model building and refinement with ISOLDE, Coot, and Phenix (phenix.real_space_refine)
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 39.595
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2300 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v4.5 IMAGE ACQUISITION EPU v3.6.0 CTF CORRECTION cryoSPARC v4.5 MODEL FITTING UCSF ChimeraX v1.8 INITIAL EULER ASSIGNMENT cryoSPARC v4.5 FINAL EULER ASSIGNMENT cryoSPARC v4.5 CLASSIFICATION RELION v5.0 RECONSTRUCTION cryoSPARC v4.5 MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 7651843