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Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.4018 f_angle_d 0.6008 f_chiral_restr 0.036 f_plane_restr 0.0041 f_bond_d 0.0032
Sample Outer kinetochore Dam1 protomer dimer with staple and Ndc80-Nuf2 coiled-coils
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 248732 Reported Resolution (Å) 3.15 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value 540.98 Fitting Procedure Details Initial rigid body fitting was performed in chimera, with manual correction in coot and real-space refinement in PHENIX
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) 1200 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL FITTING UCSF Chimera 1.12 MODEL FITTING Coot 0.9.3 MODEL REFINEMENT PHENIX dev-4620-000 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.2 INITIAL EULER ASSIGNMENT RELION 4.0-dev FINAL EULER ASSIGNMENT cryoSPARC 4.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION