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Cryo-EM structure of the MMM ubiquitin ligase complex with nanobody 992 (Composite map)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.444 f_angle_d 0.504 f_chiral_restr 0.044 f_bond_d 0.004 f_plane_restr 0.004
Sample Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992 Sample Components MOSMO MEGF8 Nanobody 992 MGRN1
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 187459 Reported Resolution (Å) 3.5 Resolution Method OTHER Other Details Using map alone (d99), resolution was estimated in Phenix real-space refinement of the composite map. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9QRU) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 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) 1600 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 PARTICLE SELECTION cryoSPARC 4.3.1 RECONSTRUCTION cryoSPARC 4.5.1
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. 1959769 Blob picker initially was used to pick particles containing a detergent micelle.