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Structure of the human mitochondrial pyruvate carrier inhibited by zaprinast
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 17.265 r_long_range_B_refined 17.264 r_dihedral_angle_3_deg 11.06 r_mcangle_it 6.811 r_mcangle_other 6.809 r_dihedral_angle_1_deg 5.277 r_scangle_other 5.142 r_dihedral_angle_2_deg 4.512 r_mcbond_it 3.702 r_mcbond_other 3.699
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 17.265 r_long_range_B_refined 17.264 r_dihedral_angle_3_deg 11.06 r_mcangle_it 6.811 r_mcangle_other 6.809 r_dihedral_angle_1_deg 5.277 r_scangle_other 5.142 r_dihedral_angle_2_deg 4.512 r_mcbond_it 3.702 r_mcbond_other 3.699 r_scbond_it 2.546 r_scbond_other 2.545 r_angle_refined_deg 1.38 r_angle_other_deg 0.505 r_chiral_restr 0.074 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 zaprinast with a pro-macrobody Sample Components Mitochondrial pyruvate carrier (MPC1L/MPC2) Pro-macrobody (fusion of a nanobody with Maltose-binding protein)
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 295345 Reported Resolution (Å) 3.92 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) 53.44
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 1739679