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BtuB3G3 bound to cyanocobalamin with disordered EL8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OKV in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.9295 f_angle_d 0.5646 f_chiral_restr 0.0458 f_plane_restr 0.0041 f_bond_d 0.0037
Sample Complex of TonB-dependent transporter BtuB3 with surface lipoprotein BtuG3 bound to cyanocobalamin (state 2)
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 91067 Reported Resolution (Å) 2.75 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (8OKV) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 35.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2300 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.1.2 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.1.2 MODEL FITTING PHENIX 1.20.1_4487 MODEL REFINEMENT PHENIX 1.20.1_4487 INITIAL EULER ASSIGNMENT cryoSPARC 4.1.2 FINAL EULER ASSIGNMENT cryoSPARC 4.1.2 RECONSTRUCTION cryoSPARC 4.1.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3311038