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Structure of the human mitochondrial late-stage transcription initiation complex, IC8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ERP
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.442 f_angle_d 0.862 f_chiral_restr 0.049 f_plane_restr 0.009 f_bond_d 0.005
Sample Structure of the human mitochondrial late-stage transcription initiation complex, IC8
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 147533 Reported Resolution (Å) 2.71 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6ERP) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation Coefficient Overall B Value Fitting Procedure Details Initial docking of the starting model was done in Chimera and flexible/refined fitting done with Coot, and Phenix Real-Space Refinement.
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 45.44
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 3200 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 Preliminary grid screening performed manually using TFS Glacios.
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.6.0 IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC 4.6.0 MODEL FITTING Coot 0.9.8.2 MODEL REFINEMENT PHENIX 1.21rc1_5015 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.0 FINAL EULER ASSIGNMENT cryoSPARC 4.6.0 CLASSIFICATION cryoSPARC 4.6.0 RECONSTRUCTION cryoSPARC 4.6.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 5354890 Automated particle picking (Blob picker, CryoSPARC) with manual inspection (Inspect Particle Picks).