☰ Navigation Tabs
Cryo-EM structure of the helix-stabilized MMM ubiquitin ligase complex with nanobody 270 (Composite map)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QRU experimental model PDB 9QS3
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.266 f_angle_d 0.436 f_chiral_restr 0.042 f_plane_restr 0.003 f_bond_d 0.002
Sample Helix-stabilized human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270 Sample Components MOSMO Helix-stabilized MEGF8 Nanobody 270 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 191977 Reported Resolution (Å) 3.3 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, 9QS3) 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 RECONSTRUCTION cryoSPARC
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. 5097418 Particles initially picked from 2D templates (imported from EMD-53323 dataset).