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Single particle cryo-EM structure of the homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P5S
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.416 r_long_range_B_other 14.416 r_dihedral_angle_3_deg 13.867 r_scangle_other 11.004 r_mcangle_it 8.741 r_mcangle_other 8.741 r_scbond_it 6.936 r_scbond_other 6.935 r_mcbond_it 5.958 r_mcbond_other 5.958
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.416 r_long_range_B_other 14.416 r_dihedral_angle_3_deg 13.867 r_scangle_other 11.004 r_mcangle_it 8.741 r_mcangle_other 8.741 r_scbond_it 6.936 r_scbond_other 6.935 r_mcbond_it 5.958 r_mcbond_other 5.958 r_dihedral_angle_1_deg 5.8 r_dihedral_angle_2_deg 3.707 r_angle_refined_deg 1.171 r_angle_other_deg 0.355 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_bond_other_d r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Sample Homohexameric 2-oxoglutarate dehydrogenase
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 1474608 Reported Resolution (Å) 2.17 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D3
Map-Model Fitting and Refinement Id 1 (8P5S) Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 40
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 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 EPU CTF CORRECTION cryoSPARC MODEL FITTING PHENIX INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC MODEL REFINEMENT REFMAC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION