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An auto inhibitory loop in the MiDAC histone deacetylase complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z2J
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.558 f_angle_d 0.475 f_chiral_restr 0.037 f_plane_restr 0.004 f_bond_d 0.003
Sample Dimeric complex of HDAC1:MIDEAS:DNTTIP1
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 305895 Reported Resolution (Å) 2.92 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6Z2J) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value 100.7 Fitting Procedure Details Initial model was built using Modelangelo and compared with PDB entry 6Z2J
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 46.7
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2400 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.4.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.4.1 MODEL FITTING Coot 0.9.6 MODEL REFINEMENT PHENIX 1.21.1_5286 FINAL EULER ASSIGNMENT cryoSPARC 4.4.1 CLASSIFICATION cryoSPARC 4.4.1 RECONSTRUCTION cryoSPARC 4.4.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3618574