9PDQ | pdb_00009pdq

Human OCTN2 bound to carnitine in the occluded conformation


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldO76082 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.1003
f_angle_d0.5394
f_chiral_restr0.0391
f_plane_restr0.0057
f_bond_d0.003
Sample
Novel organic cation transport 2 (OCTN2;SLC22A5) bound to carnitine in the occluded conformation.
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles181269
Reported Resolution (Å)2.72
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)82
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 CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.6
IMAGE ACQUISITIONEPU2.14
MODEL FITTINGISOLDE1.8
MODEL FITTINGCoot0.9.8.94
INITIAL EULER ASSIGNMENTcryoSPARC4.6
FINAL EULER ASSIGNMENTcryoSPARC4.6
CLASSIFICATIONcryoSPARC4.6
RECONSTRUCTIONcryoSPARC4.6
MODEL REFINEMENTPHENIX1.21.1_5286
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY6410000