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Cryo-EM structure of the CO dehydrogenase (CODH) subcomplex from Methanosarcina acetivorans
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 3.9151 f_angle_d 0.6517 f_chiral_restr 0.0392 f_plane_restr 0.0035 f_bond_d 0.0022
Sample CO dehydrogenase (CODH) isoform Cdh2
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details blotted with blot force 4 for 4 s
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 187510 Reported Resolution (Å) 3.55 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value 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 JEOL CRYO ARM 200 Minimum Defocus (nm) 500 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4 CTF CORRECTION cryoSPARC 4 MODEL FITTING Coot 0.9.8.96 RECONSTRUCTION cryoSPARC 5 MODEL REFINEMENT PHENIX 2.0_5936
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 371631