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Cryo-EM structure of human glycerol-3-phosphate acyltransferase 1 (GPAT1) in complex with CoA and palmitoyl-LPA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8E4Y
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.484 r_long_range_B_refined 16.323 r_long_range_B_other 16.322 r_dihedral_angle_3_deg 13.402 r_dihedral_angle_4_deg 11.187 r_mcangle_it 10.049 r_mcangle_other 10.048 r_scangle_other 9.787 r_mcbond_other 6.081 r_mcbond_it 6.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.484 r_long_range_B_refined 16.323 r_long_range_B_other 16.322 r_dihedral_angle_3_deg 13.402 r_dihedral_angle_4_deg 11.187 r_mcangle_it 10.049 r_mcangle_other 10.048 r_scangle_other 9.787 r_mcbond_other 6.081 r_mcbond_it 6.08 r_dihedral_angle_1_deg 5.704 r_scbond_it 5.652 r_scbond_other 5.651 r_angle_refined_deg 1.275 r_angle_other_deg 1.014 r_chiral_restr 0.045 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 glycerol-3-phosphate acyltransferase 1
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot force -5, blot time 3 sec
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 76033 Reported Resolution (Å) 3.67 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (8E4Y) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 78
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 600 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT RELION 3.1.2 FINAL EULER ASSIGNMENT RELION 3.1.2 RECONSTRUCTION RELION 3.1.2 MODEL REFINEMENT PHENIX MODEL REFINEMENT REFMAC 5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1704123