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Dot1L bound to the H2BK120 Ubiquitinated nucleosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NW3 experimental model PDB 1UBQ experimental model PDB 3TU4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.597 f_angle_d 0.966 f_chiral_restr 0.056 f_bond_d 0.011 f_plane_restr 0.008
Sample 3.5 angstroms Dot1L-H2BK120Ub Sample 1A Sample Components Ubiquitinated Nucleosome Histone-lysine N-methyltransferase H3 lysine-79 specific Ubiquitin Histone octamer DNA 146-MER
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name PROPANE Sample Vitrification Details blotted for 3s before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 211279 Reported Resolution (Å) 3.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (1NW3, 1UBQ, 3TU4) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value 91.61 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 1.1
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1700 Maximum Defocus (nm) 3200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION Scipion CTF CORRECTION Gctf v1 MODEL FITTING UCSF Chimera 1.13.1 CLASSIFICATION RELION RECONSTRUCTION cisTEM MODEL REFINEMENT PHENIX 1.14
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION