8S5W

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

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.887
r_dihedral_angle_6_deg	16.736
r_dihedral_angle_1_deg	4.611
r_angle_refined_deg	1.329
r_dihedral_angle_2_deg	0.852
r_angle_other_deg	0.586
r_symmetry_nbd_other	0.225
r_nbd_refined	0.212
r_nbtor_refined	0.209
r_xyhbond_nbd_refined	0.176
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.051
r_symmetry_xyhbond_nbd_other	0.023
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002
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:fedratinib
Sample Components
SLC19A3
Nb3.7

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	378839
Reported Resolution (Å)	3.05
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	45

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC
MODEL FITTING	ISOLDE
MODEL REFINEMENT	PHENIX
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION