8P5T

Single particle cryo-EM structure of the homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined14.416
r_long_range_B_other14.416
r_dihedral_angle_3_deg13.867
r_scangle_other11.004
r_mcangle_it8.741
r_mcangle_other8.741
r_scbond_it6.936
r_scbond_other6.935
r_mcbond_it5.958
r_mcbond_other5.958
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined14.416
r_long_range_B_other14.416
r_dihedral_angle_3_deg13.867
r_scangle_other11.004
r_mcangle_it8.741
r_mcangle_other8.741
r_scbond_it6.936
r_scbond_other6.935
r_mcbond_it5.958
r_mcbond_other5.958
r_dihedral_angle_1_deg5.8
r_dihedral_angle_2_deg3.707
r_angle_refined_deg1.171
r_angle_other_deg0.355
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_gen_planes_other0.001
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 StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1474608
Reported Resolution (Å)2.17
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD3
Map-Model Fitting and Refinement
Id1 (8P5S)
Refinement Space
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC
MODEL FITTINGPHENIX
INITIAL EULER ASSIGNMENTcryoSPARC
FINAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONcryoSPARC
MODEL REFINEMENTREFMAC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION