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Human dysferlin (1-2017) in the lipid-free, Ca2+-bound state
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 6.1725 f_angle_d 0.9155 f_chiral_restr 0.0521 f_plane_restr 0.008 f_bond_d 0.0038
Sample Lipid-free human dysferlin (1-2017) in the Ca2+-bound state
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 29793 Reported Resolution (Å) 3.54 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 AB INITIO MODEL Refinement Target Overall B Value 162.24 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 40.184
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 v.4.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC v.4.1 MODEL FITTING UCSF Chimera v.1.16 MODEL FITTING ISOLDE INITIAL EULER ASSIGNMENT cryoSPARC v.4.1 FINAL EULER ASSIGNMENT cryoSPARC v.4.1 CLASSIFICATION RELION v.4.0 RECONSTRUCTION cryoSPARC v.4.1 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 2861382