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CryoEM structure of the Themis:Grb2 complex with bound ProMacrobody 256
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold in silico model Other experimental model PDB 7OMT
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.717 f_angle_d 0.528 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.002
Sample Themis-Grb2 complex bound to ProMacrobody 256
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details Leica EM GP2, 5 s blotting time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 601216 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7OMT) Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 61.8
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 Minimum Defocus (nm) 1400 Maximum Defocus (nm) 1900 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 60000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v4.5.1 PARTICLE SELECTION crYOLO IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC v4.5.1 MODEL FITTING UCSF ChimeraX 1.8 MODEL FITTING NAMD INITIAL EULER ASSIGNMENT cryoSPARC v4.5.1 FINAL EULER ASSIGNMENT cryoSPARC v4.5.1 CLASSIFICATION cryoSPARC v4.5.1 RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.21.1_5286:
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION