8P5W

Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum following reaction with the 2-oxoglutarate analogue succinyl phosphonate


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.505
r_long_range_B_refined12.251
r_long_range_B_other12.251
r_scangle_other9.109
r_mcangle_it7.208
r_mcangle_other7.208
r_dihedral_angle_1_deg5.824
r_scbond_it5.508
r_scbond_other5.508
r_mcbond_it4.489
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.505
r_long_range_B_refined12.251
r_long_range_B_other12.251
r_scangle_other9.109
r_mcangle_it7.208
r_mcangle_other7.208
r_dihedral_angle_1_deg5.824
r_scbond_it5.508
r_scbond_other5.508
r_mcbond_it4.489
r_mcbond_other4.489
r_dihedral_angle_2_deg3.336
r_angle_refined_deg1.011
r_angle_other_deg0.315
r_chiral_restr0.051
r_bond_refined_d0.005
r_gen_planes_refined0.003
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 Particles646352
Reported Resolution (Å)2.26
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD3
Map-Model Fitting and Refinement
Id1 (8P5T)
Refinement SpaceREAL
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)2200
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
MODEL REFINEMENTREFMAC
INITIAL EULER ASSIGNMENTcryoSPARC
FINAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION