☰ Navigation Tabs
Integrin alpha-5 beta-1 in complex with BIIG2 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VI3
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.587 f_angle_d 0.524 f_chiral_restr 0.042 f_bond_d 0.004 f_plane_restr 0.003
Sample Protein complex of integrin alpha-5 beta-1 with BIIG2 Fab
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 317066 Reported Resolution (Å) 2.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (3VI3, 3VI3) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation coefficient Overall B Value 93 Fitting Procedure Details Initial local fitting was done using ChimeraX and then Phenix, ISOLDE and COOT for flexible fitting and modeling.
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 TFS GLACIOS Minimum Defocus (nm) 1400 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 36000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC MODEL FITTING PHENIX MODEL FITTING UCSF ChimeraX MODEL REFINEMENT PHENIX MODEL REFINEMENT ISOLDE MODEL REFINEMENT Coot INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2425530