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Cryo-EM structure of coproheme decarboxylase from Corynebacterium diphtheriae in complex with heme b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XUC
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.4523 f_angle_d 0.5583 f_chiral_restr 0.0415 f_plane_restr 0.0033 f_bond_d 0.0025
Sample Coproheme decarboxylase from Corynebacterium diphteriae in complex with heme b
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blotting time; 5.0-5.5 s.
Blotting force; 18 or 19
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 870660 Reported Resolution (Å) 1.94 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C5
Map-Model Fitting and Refinement Id 1 (6XUC) Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 72
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 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 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC MODEL FITTING MOLREP MODEL REFINEMENT REFMAC MODEL REFINEMENT PHENIX CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION