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Structure of two nucleosomes bridged by human PARP2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F5B experimental model PDB 5Y0C experimental model PDB 6R1T
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 26.8363 f_angle_d 1.9379 f_chiral_restr 0.0942 f_plane_restr 0.0203 f_bond_d 0.0148
Sample Two nucleosomes bridged by PARP2 Sample Components histone DNA PARP2
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot time 2s, blot force 0
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 27889 Reported Resolution (Å) 10.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6F5B, 6F5B, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 5Y0C, 6R1T, 6R1T) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Real-space CC Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 56.1
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI F30 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION Gctf 1.06 MODEL FITTING UCSF Chimera 1.13.1 MODEL REFINEMENT PHENIX 1.17-3644 INITIAL EULER ASSIGNMENT RELION 3.0 FINAL EULER ASSIGNMENT RELION 3.0 CLASSIFICATION RELION 3.0 RECONSTRUCTION RELION 3.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 226250 Picked using crYOLO version 1.3.1 with a model trained on the same dataset (with the generic model provided with crYOLO used as pre-trained weights).