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Single particle cryo-EM structure of the complex between Corynebacterium glutamicum homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-protein inhibitor OdhI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P5T experimental model PDB 4QCJ
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.304 r_dihedral_angle_4_deg 15.333 r_dihedral_angle_3_deg 13.946 r_long_range_B_refined 13.453 r_long_range_B_other 13.453 r_scangle_other 9.722 r_mcangle_it 8.097 r_mcangle_other 8.097 r_scbond_it 6.172 r_scbond_other 6.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.304 r_dihedral_angle_4_deg 15.333 r_dihedral_angle_3_deg 13.946 r_long_range_B_refined 13.453 r_long_range_B_other 13.453 r_scangle_other 9.722 r_mcangle_it 8.097 r_mcangle_other 8.097 r_scbond_it 6.172 r_scbond_other 6.172 r_dihedral_angle_1_deg 6.113 r_mcbond_it 5.446 r_mcbond_other 5.446 r_angle_refined_deg 1.441 r_angle_other_deg 1.122 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 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 Complex of homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-domain inhibitor OdhI
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 958690 Reported Resolution (Å) 2.29 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D3
Map-Model Fitting and Refinement Id 1 (8P5T, 4QCJ) Refinement Space REAL 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) 2200 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 RECONSTRUCTION cryoSPARC MODEL REFINEMENT REFMAC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION