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Cryo-EM structure of human integrin alpha5beta1 in complex with fibronectin (FN 7-10)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VI3 experimental model PDB 1FNF
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.441 f_angle_d 0.693 f_chiral_restr 0.05 f_plane_restr 0.005 f_bond_d 0.003
Sample integrin a5b1-fibronectin complex
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 130907 Reported Resolution (Å) 2.61 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (3vi3, 1fnf) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details initial rigid body fitting in chimera, then cycles of manual adjustment/modeling in coot and real-space refinement in phenix
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 69
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS 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 PARTICLE SELECTION Gautomatch IMAGE ACQUISITION SerialEM CTF CORRECTION RELION 3.0 MODEL FITTING UCSF Chimera MODEL FITTING Coot INITIAL EULER ASSIGNMENT RELION 3.0 FINAL EULER ASSIGNMENT RELION 3.0 CLASSIFICATION RELION RECONSTRUCTION RELION 3.0 MODEL REFINEMENT Coot MODEL REFINEMENT PHENIX 1.21_5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2640989