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Cryo-EM structure of VCPIP1 VCPID bound to VCP D2 domain dimer (with extra D2 domain)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FTK in silico model AlphaFold AF-Q8CDG3-F1-v4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.649 f_angle_d 0.4914 f_chiral_restr 0.0415 f_plane_restr 0.0038 f_bond_d 0.0028
Sample Complex of valosin containing protein (VCP)/p97 and valosin containing protein interacting protein 1 (VCPIP1) Sample Components Valosin containing protein interacting domain (VCPID) with connecting residues of VCPIP1 stalk region Valosin containing protein (VCP) D2 Domain
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 592034 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (5FTK) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 53.69
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 900 Maximum Defocus (nm) 2200 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO IMAGE ACQUISITION SerialEM 3.8.6 CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING UCSF ChimeraX 1.6 MODEL FITTING ISOLDE INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 4.6.0 RECONSTRUCTION cryoSPARC 4.6.0 MODEL REFINEMENT 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 2050250