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Cryo-EM Structures of Full-length Integrin alphaIIbbeta3 in Native Lipids complexed with Eptifibatide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VDN
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 40.306 r_long_range_B_other 40.304 r_dihedral_angle_2_deg 33.58 r_mcangle_it 25.317 r_mcangle_other 25.316 r_scangle_other 22.032 r_dihedral_angle_3_deg 18.737 r_dihedral_angle_4_deg 16.6 r_mcbond_it 15.821 r_mcbond_other 15.817
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 40.306 r_long_range_B_other 40.304 r_dihedral_angle_2_deg 33.58 r_mcangle_it 25.317 r_mcangle_other 25.316 r_scangle_other 22.032 r_dihedral_angle_3_deg 18.737 r_dihedral_angle_4_deg 16.6 r_mcbond_it 15.821 r_mcbond_other 15.817 r_scbond_it 13.331 r_scbond_other 13.33 r_dihedral_angle_1_deg 7.104 r_angle_refined_deg 1.479 r_angle_other_deg 1.383 r_chiral_restr 0.068 r_bond_other_d 0.016 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 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 integrin alphaIIbbeta3 with eptifibatide
Specimen Preparation Sample Aggregation State CELL Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 268647 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (2VDN) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.27 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.2.1 CTF CORRECTION cryoSPARC 4.2.1 MODEL FITTING PHENIX 1.20.1 INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1 FINAL EULER ASSIGNMENT cryoSPARC 4.2.1 CLASSIFICATION cryoSPARC 4.2.1 RECONSTRUCTION cryoSPARC 4.2.1 MODEL REFINEMENT PHENIX 1.20.1 MODEL REFINEMENT REFMAC 5.8.0267
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2645177