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SAGA DUB module bound to a ubiqitinated nucleosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZUX
Sample SAGA DUB-ubiqitinated nucleosome complex Sample Components nucleosome SAGA DUB module DNA Ubiquitin carboxyl-terminal hydrolase 8 ubiquitin
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot for 4 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 113856 Reported Resolution (Å) 3.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4ZUX) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value 114.6 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 44.17
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION Warp 1.0.6 MODEL FITTING Coot 0.8.9 FINAL EULER ASSIGNMENT RELION 3.0.5 RECONSTRUCTION RELION 3.0.5 MODEL REFINEMENT PHENIX 1.16
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 313986