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Cryo-EM structure of synthetic tetrameric building block sC4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.382 f_angle_d 0.861 f_chiral_restr 0.044 f_bond_d 0.007 f_plane_restr 0.003
Sample De novo designed tetramer sC4
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot time = 4s
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 378829 Reported Resolution (Å) 3.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C4
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 224.3 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 47.07
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2000 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 2.0 IMAGE ACQUISITION Leginon 3.0 CTF CORRECTION cryoSPARC 2.0 CTF CORRECTION CTFFIND MODEL FITTING UCSF Chimera 1.13 INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT RELION 3.0 CLASSIFICATION RELION 3.0 RECONSTRUCTION RELION 3.0 MODEL REFINEMENT PHENIX 1.16 MODEL REFINEMENT Coot 0.8.9.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3781336