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Antibody fragment from mAb824 bound to the adhesin protein FimH.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JWN experimental model PDB 15C8
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.342 f_angle_d 0.59 f_chiral_restr 0.045 f_plane_restr 0.005 f_bond_d 0.004
Sample Antibody fragment from mAb824 bound to the E. coli adhesin protein FimH Sample Components Fimbrial tip Antibody Fragments
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument HOMEMADE PLUNGER Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 306269 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (9ME5) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 42
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 750 Maximum Defocus (nm) 1500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 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 cryoSPARC 4.7.1 IMAGE ACQUISITION SerialEM 4.1 CTF CORRECTION cryoSPARC 4.5.3 MODEL FITTING UCSF ChimeraX 1.9 MODEL FITTING ISOLDE 1.6 MODEL REFINEMENT PHENIX 1.21.1_5286 INITIAL EULER ASSIGNMENT cryoSPARC 4.5.3 FINAL EULER ASSIGNMENT RELION 5.0 RECONSTRUCTION PHENIX 1.21.1-5286
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION