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Structure of the human mitochondrial pyruvate carrier in the apo-state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other D_1292140991
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.602 r_long_range_B_other 8.322 r_long_range_B_refined 8.321 r_dihedral_angle_1_deg 5.127 r_dihedral_angle_2_deg 3.849 r_mcangle_it 2.851 r_mcangle_other 2.85 r_scangle_other 2.061 r_mcbond_it 1.536 r_mcbond_other 1.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.602 r_long_range_B_other 8.322 r_long_range_B_refined 8.321 r_dihedral_angle_1_deg 5.127 r_dihedral_angle_2_deg 3.849 r_mcangle_it 2.851 r_mcangle_other 2.85 r_scangle_other 2.061 r_mcbond_it 1.536 r_mcbond_other 1.535 r_angle_refined_deg 1.304 r_scbond_it 1.023 r_scbond_other 1.022 r_angle_other_deg 0.447 r_chiral_restr 0.062 r_bond_refined_d 0.004 r_gen_planes_refined 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 apo human mitochondrial pyruvate carrier (MPC1L/MPC2) 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 164876 Reported Resolution (Å) 3.65 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) 54.44
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 1329798