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Cryo-EM structure of the binary MEGF8-MOSMO complex with nanobody 270
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QQS
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.462 f_angle_d 0.492 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.002
Sample Human MEGF8-MOSMO binary complex bound to nanobody 270 Sample Components MOSMO MEGF8 Nanobody 270
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 228513 Reported Resolution (Å) 2.98 Resolution Method FSC 0.143 CUT-OFF Other Details Local refinement with a mask containing MEGF8, MOSMO and nanobody 270 was performed after non-uniform refinement, to mask out the micelle. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9QQS) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 143.4 Fitting Procedure Details Initial local fitting was done using ChimeraX then manual model building in Coot was interspersed with real space refinement in Phenix.
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1400 Maximum Defocus (nm) 2600 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 MODEL REFINEMENT PHENIX 1.21rc1_5156:
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF estimation was performed in cryoSPARC live pre-processing. 2266859 Template picker using 2D classes from a screening dataset collected on a different grid.