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Cryo-EM structure of YiiP-Fab complex in Apo state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VRF
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.6961 f_angle_d 0.7537 f_chiral_restr 0.0451 f_bond_d 0.006 f_plane_restr 0.0056
Sample YiiP_SO in complex with Fab2R Sample Components YiiP Fab2R_light chain Fab2R_heavy chain
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3ul of protein mixture applied to grid. Blot time 4 seconds, blot force 0.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 140565 Reported Resolution (Å) 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 (5VRF) Refinement Space REAL Refinement Protocol BACKBONE TRACE Refinement Target cross-correlation Overall B Value 101 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 65
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 2.90 CTF CORRECTION cryoSPARC 2.9.0 MODEL FITTING UCSF Chimera 1.13.1 INITIAL EULER ASSIGNMENT cryoSPARC 2.9.0 FINAL EULER ASSIGNMENT cryoSPARC 2.9.0 CLASSIFICATION cryoSPARC 2.9.0 RECONSTRUCTION cryoSPARC 2.9.0 MODEL REFINEMENT PHENIX 1.18
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 848576