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Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9S4Q experimental model PDB 9S53
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.182 f_angle_d 0.446 f_chiral_restr 0.036 f_bond_d 0.018 f_plane_restr 0.003
Sample Saccharomyces cerevisiae outer kinetochore KMN junction complex Sample Components Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex Saccharomyces cerevisiae outer kinetochore Ndc80c
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 18160 Reported Resolution (Å) 7.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refined using Blush regularization Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (9S4Q, 9S4Q, 9S4Q, 9S53, 9S4Q, 9S53, 9S4Q, 9S4Q, 9S4Q, 9S4Q) Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1400 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF ChimeraX MODEL FITTING Coot INITIAL EULER ASSIGNMENT RELION 5 FINAL EULER ASSIGNMENT RELION 5 RECONSTRUCTION RELION 5 MODEL REFINEMENT PHENIX 1.21.2_5419:
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2592458 Selected using Topaz particle picker trained on manually picked micrographs