9LUB | pdb_00009lub

The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 2


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined31.196
r_long_range_B_other31.195
r_scangle_other21.798
r_dihedral_angle_3_deg20.965
r_dihedral_angle_2_deg18.845
r_mcangle_it15.515
r_mcangle_other15.515
r_scbond_it12.743
r_scbond_other12.742
r_mcbond_it9.369
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined31.196
r_long_range_B_other31.195
r_scangle_other21.798
r_dihedral_angle_3_deg20.965
r_dihedral_angle_2_deg18.845
r_mcangle_it15.515
r_mcangle_other15.515
r_scbond_it12.743
r_scbond_other12.742
r_mcbond_it9.369
r_mcbond_other9.364
r_dihedral_angle_1_deg5.277
r_angle_refined_deg1.56
r_angle_other_deg0.516
r_chiral_restr0.085
r_bond_refined_d0.007
r_gen_planes_refined0.007
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
The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles69957
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
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)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.073
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification59000
Calibrated Magnification56818
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.8
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC3.8
MODEL FITTINGCoot
MODEL REFINEMENTServalcat
INITIAL EULER ASSIGNMENTcryoSPARC3.8
FINAL EULER ASSIGNMENTcryoSPARC3.8
CLASSIFICATIONcryoSPARC3.8
RECONSTRUCTIONcryoSPARC3.8
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION765007