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Cryo-EM structure of designed protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BY7 experimental model PDB 2LW9
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.3452 f_angle_d 0.4693 f_chiral_restr 0.0417 f_plane_restr 0.0031 f_bond_d 0.0022
Sample 60-meric complex of designed fusion proteins TIP60
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 115596 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (3BY7, 2LW9) Refinement Space REAL Refinement Protocol BACKBONE TRACE Refinement Target Correlation coefficient Overall B Value 205.47 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 500 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1 CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF Chimera MODEL FITTING Coot INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 1.19
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 175419