8P5X | pdb_00008p5x

Single particle cryo-EM structure of the complex between Corynebacterium glutamicum homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-protein inhibitor OdhI


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8P5T 
experimental modelPDB 4QCJ 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.304
r_dihedral_angle_4_deg15.333
r_dihedral_angle_3_deg13.946
r_long_range_B_refined13.453
r_long_range_B_other13.453
r_scangle_other9.722
r_mcangle_it8.097
r_mcangle_other8.097
r_scbond_it6.172
r_scbond_other6.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.304
r_dihedral_angle_4_deg15.333
r_dihedral_angle_3_deg13.946
r_long_range_B_refined13.453
r_long_range_B_other13.453
r_scangle_other9.722
r_mcangle_it8.097
r_mcangle_other8.097
r_scbond_it6.172
r_scbond_other6.172
r_dihedral_angle_1_deg6.113
r_mcbond_it5.446
r_mcbond_other5.446
r_angle_refined_deg1.441
r_angle_other_deg1.122
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_gen_planes_other0.002
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 StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles958690
Reported Resolution (Å)2.29
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD3
Map-Model Fitting and Refinement
Id1 (8P5T, 4QCJ)
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
INITIAL EULER ASSIGNMENTcryoSPARC
FINAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTREFMAC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION