8S5Z

Cryo-EM structure of hydroxychloroquine-bound human SLC19A3 in inward-open state


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.907
r_dihedral_angle_6_deg16.9
r_dihedral_angle_1_deg4.036
r_angle_refined_deg1.361
r_angle_other_deg0.904
r_dihedral_angle_2_deg0.559
r_nbd_refined0.233
r_symmetry_nbd_other0.221
r_nbtor_refined0.211
r_xyhbond_nbd_refined0.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.907
r_dihedral_angle_6_deg16.9
r_dihedral_angle_1_deg4.036
r_angle_refined_deg1.361
r_angle_other_deg0.904
r_dihedral_angle_2_deg0.559
r_nbd_refined0.233
r_symmetry_nbd_other0.221
r_nbtor_refined0.211
r_xyhbond_nbd_refined0.157
r_symmetry_nbtor_other0.084
r_chiral_restr0.054
r_gen_planes_other0.011
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_lrange_it
r_lrange_other
Sample
SLC19A3:Nb3.7:hydroxychloroquine
Sample Components
SLC19A3
Nb3.3
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles249857
Reported Resolution (Å)3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)58
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)2700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification215000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC
MODEL FITTINGISOLDE
MODEL REFINEMENTPHENIX
INITIAL EULER ASSIGNMENTcryoSPARC
FINAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION