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Structure of E. coli WbaP in complex with a megabody in presence of UDP-Gal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9S7S
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.043 f_angle_d 0.453 f_chiral_restr 0.036 f_plane_restr 0.003 f_bond_d 0.002
Sample Complex of dimeric WbaP with 2 megabody molecules Sample Components WbaP Megabody
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 225535 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9S7S) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF Chimera MODEL FITTING Coot INITIAL EULER ASSIGNMENT RELION FINAL EULER ASSIGNMENT RELION CLASSIFICATION RELION RECONSTRUCTION RELION MODEL REFINEMENT PHENIX 1.20.1_4487:
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2293857