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Cryo-EM structure of human integrin alpha5beta1 in the half-bent conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WK0 experimental model PDB 3VI3 experimental model PDB 3FCS
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.557 f_angle_d 1.48 f_chiral_restr 0.194 f_plane_restr 0.029 f_bond_d 0.013
Sample Dimeric complex of integrin a5b1
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 98750 Reported Resolution (Å) 4.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4WK0, 4WK0, 3VI3, 3VI3, 3FCS, 3FCS) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 65.8 82.3
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) -500 Maximum Defocus (nm) 3200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.62 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION Gctf MODEL FITTING UCSF Chimera MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT RELION 3.0 CLASSIFICATION RELION 3.0 RECONSTRUCTION RELION 3.0 MODEL REFINEMENT Coot MODEL REFINEMENT PHENIX 1.17.1 Release 3660
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 496356 1424 particles were manually picked and used to obtain 2D classes with distinct features as templates for Gautomatch