9UD4 | pdb_00009ud4

Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-T236Y mutant from Vibrio cholerae reduced by NADH


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7XK3 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d8.057
f_angle_d0.537
f_chiral_restr0.042
f_plane_restr0.005
f_bond_d0.003
Sample
Na(+)-translocating NADH-quinone reductase
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles319845
Reported Resolution (Å)3.31
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7XK3)
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)65
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.029
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARCv3.3.1
IMAGE ACQUISITIONSerialEM4
CTF CORRECTIONcryoSPARCv3.3.1
MODEL FITTINGCoot0.9
INITIAL EULER ASSIGNMENTcryoSPARCv3.3.1
FINAL EULER ASSIGNMENTcryoSPARCv3.3.1
CLASSIFICATIONcryoSPARCv3.3.1
RECONSTRUCTIONcryoSPARCv3.3.1
MODEL REFINEMENTPHENIX1.21.1_5286
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE2496421