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HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BE8 experimental model PDB 2MPT other Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.535 f_angle_d 0.503 f_chiral_restr 0.038 f_bond_d 0.003 f_plane_restr 0.003
Sample HECT domain of NEDD4-2
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Vitrification carried out at Argon atmosphere
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 90979 Reported Resolution (Å) 3.06 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4BE8, 2MPT) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details The initial local fitting was done using UCSF Chimera and proceed to use real space fitting to complete the whole assembly in Coot
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 1.092
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 2500 Maximum Defocus (nm) 2500 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Preliminary grid screening was performed manually
EM Software Task Software Package Version PARTICLE SELECTION Topaz 0.26a IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC MODEL FITTING UCSF ChimeraX version 1.9.dev202409060131 (2024-09-06) MODEL FITTING Coot 0.9.6.EL MODEL REFINEMENT PHENIX v1.21-5207 RECONSTRUCTION cryoSPARC v4.4
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE We generated ab initio reconstruction model in CryoSPARC and use it in our pipeline 1631714