8JF0

Human sodium-dependent vitamin C transporter 1 in an intermediate state


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8JEZ 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined49.924
r_long_range_B_other49.923
r_dihedral_angle_2_deg34.819
r_scangle_other25.486
r_mcangle_it24.414
r_mcangle_other24.409
r_dihedral_angle_4_deg17.714
r_scbond_it15.047
r_scbond_other15.043
r_mcbond_other14.672
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined49.924
r_long_range_B_other49.923
r_dihedral_angle_2_deg34.819
r_scangle_other25.486
r_mcangle_it24.414
r_mcangle_other24.409
r_dihedral_angle_4_deg17.714
r_scbond_it15.047
r_scbond_other15.043
r_mcbond_other14.672
r_mcbond_it14.67
r_dihedral_angle_3_deg11.765
r_dihedral_angle_1_deg3.38
r_angle_other_deg1.629
r_angle_refined_deg1.329
r_chiral_restr0.08
r_gen_planes_refined0.014
r_gen_planes_other0.01
r_bond_refined_d0.009
r_bond_other_d0.006
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
Human SVCT1 dimer in an intermediate state
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles149304
Reported Resolution (Å)3.5
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (8JEZ)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50.9
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1.1
IMAGE ACQUISITIONEPU1.24.2
CTF CORRECTIONRELION3.1.1
MODEL FITTINGCoot0.9.6
INITIAL EULER ASSIGNMENTRELION3.1.1
FINAL EULER ASSIGNMENTRELION3.1.1
RECONSTRUCTIONRELION3.1.1
MODEL REFINEMENTServalcat0.2.115
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION3699304