☰ Navigation Tabs
Cryo-EM Structures of Full-length Integrin alphaIIbbeta3 in Native Lipids
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FCS experimental model PDB 2K9J
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 40.06 r_long_range_B_other 40.06 r_dihedral_angle_2_deg 34.027 r_scangle_other 27.44 r_mcangle_it 27.371 r_mcangle_other 27.369 r_mcbond_it 18.836 r_mcbond_other 18.753 r_dihedral_angle_3_deg 18.57 r_scbond_it 18.013
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 40.06 r_long_range_B_other 40.06 r_dihedral_angle_2_deg 34.027 r_scangle_other 27.44 r_mcangle_it 27.371 r_mcangle_other 27.369 r_mcbond_it 18.836 r_mcbond_other 18.753 r_dihedral_angle_3_deg 18.57 r_scbond_it 18.013 r_scbond_other 18.012 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_1_deg 7.517 r_angle_refined_deg 1.713 r_angle_other_deg 1.409 r_chiral_restr 0.071 r_bond_other_d 0.015 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 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 full length integrin alphaIIbbeta3
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 117126 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (3FCS, 2K9J) 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) 1000 Maximum Defocus (nm) 2500 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 MODEL FITTING UCSF Chimera 1.15 MODEL REFINEMENT PHENIX 1.20.1 MODEL REFINEMENT REFMAC 5.8.0267 CLASSIFICATION cryoSPARC 4.2.1 RECONSTRUCTION cryoSPARC 4.2.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4477836