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SARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C6 symmetry)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.5814 f_angle_d 0.4804 f_chiral_restr 0.0384 f_plane_restr 0.0037 f_bond_d 0.0016
Sample SARS-CoV-2 DMV nsp3-4 pore complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SUBTOMOGRAM AVERAGING Number of Particles 113163 Reported Resolution (Å) 4.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C6
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 3
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 6000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version VOLUME SELECTION emClarity v1.6.2 IMAGE ACQUISITION SerialEM CTF CORRECTION emClarity v1.6.2 CTF CORRECTION RELION v4 MODEL FITTING UCSF Chimera 1.16 MODEL FITTING UCSF ChimeraX 1.6.1 MODEL FITTING Coot 0.9.8 MODEL FITTING ISOLDE 1.6.0 FINAL EULER ASSIGNMENT RELION v4 CLASSIFICATION RELION v4 RECONSTRUCTION RELION v4 MODEL REFINEMENT PHENIX 1.21_5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION