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Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UXW
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 25.356 f_angle_d 0.759 f_chiral_restr 0.045 f_plane_restr 0.005 f_bond_d 0.004
Sample Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA) Sample Components DDM1 Nucleosome core particle Histone octamer DNA double helix
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details Blotted for 2.5 seconds before plunging.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 215066 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 (6UXW, 6UXW, 6UXW, 6UXW, 6UXW, 6UXW, 6UXW, 6UXW, 6UXW, 6UXW) Refinement Space REAL Refinement Protocol Refinement Target Correlation coefficient Overall B Value 57.8 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 71.2
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2200 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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Warp 1.0.9 IMAGE ACQUISITION EPU 2.10.0.5 CTF CORRECTION Warp 1.0.9 MODEL FITTING Coot 0.9.2-pre MODEL REFINEMENT PHENIX 1.19.2-4158-000 INITIAL EULER ASSIGNMENT cryoSPARC 3.0.2+210831 FINAL EULER ASSIGNMENT cryoSPARC 3.0.2+210831 CLASSIFICATION cryoSPARC 3.0.2+210831 RECONSTRUCTION cryoSPARC 3.0.2+210831
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 3788872