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ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold experimental model PDB 3TU4 experimental model PDB 8H1T experimental model PDB 8SVF experimental model PDB 4R8P experimental model PDB 2D9G in silico model SwissModel experimental model PDB 1UBQ experimental model PDB 7PFV
Sample ncPRC1RYBP bound to H2AK119Ub/H1.4 Chromatosome Sample Components Histones DNA ncPRC1-RYBP Ubiquitin Histone H3.2 Histone H4 Histone H2A Histone H2B 1.1 DNA (187-MER) DNA (187-MER) Polycomb complex protein BMI-1 E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3 RING1 and YY1-binding protein Histone H1.4
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 205635 Reported Resolution (Å) 3.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (3tu4, 8H1T, 8SVF, 4R8P, 2D9G, 1UBQ, 7PFV) 2 (2WWZ) 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) 61.06
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2500 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 IMAGE ACQUISITION Leginon v 3.6 MODEL FITTING UCSF ChimeraX 1.7.1 MODEL FITTING Coot 0.9.8.94 RECONSTRUCTION cryoSPARC 4.4 MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1394967