9GIY | pdb_00009giy

Structure of the human mitochondrial pyruvate carrier inhibited by mitoglitazone

ELECTRON MICROSCOPY

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	9.708
r_long_range_B_refined	7.76
r_long_range_B_other	7.76
r_dihedral_angle_1_deg	4.908
r_dihedral_angle_2_deg	4.42
r_mcangle_it	2.579
r_mcangle_other	2.579
r_scangle_other	1.642
r_mcbond_it	1.375
r_mcbond_other	1.375
r_angle_refined_deg	1.26
r_scbond_it	0.781
r_scbond_other	0.78
r_angle_other_deg	0.435
r_chiral_restr	0.06
r_gen_planes_refined	0.006
r_bond_refined_d	0.004
r_gen_planes_other	0.001
r_bond_other_d
r_dihedral_angle_4_deg
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
Complex of human mitochondrial pyruvate carrier (MPC1L/MPC2) inhibited by mitoglitazone with a pro-macrobody
Sample Components
Mitochondrial pyruvate carrier (MPC1L/MPC2)
Macrobody with C-terminal MBP tag

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	190059
Reported Resolution (Å)	3.79
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)	53.69

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	165000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Warp
IMAGE ACQUISITION	EPU
CTF CORRECTION	Warp
MODEL FITTING	Coot	0.9.8.92
MODEL FITTING	ISOLDE
MODEL FITTING	UCSF ChimeraX	1.7.1
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3.2
FINAL EULER ASSIGNMENT	cryoSPARC	3.3.2
CLASSIFICATION	cryoSPARC	3.3.2
RECONSTRUCTION	cryoSPARC	3.3.2
MODEL REFINEMENT	REFMAC	5.8.0419

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1555900