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Structure of yeast DNA Polymerase Zeta (apo)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6V8P
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.539 f_angle_d 1.299 f_chiral_restr 0.074 f_plane_restr 0.009 f_bond_d 0.006
Sample DNA polymerase Zeta
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK II Cryogen Name ETHANE Sample Vitrification Details Blot for 6 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 213120 Reported Resolution (Å) 4.11 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6V8P) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 45.7
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 48780 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM 3.9 CTF CORRECTION cryoSPARC 3.0 MODEL FITTING UCSF Chimera 1.14 MODEL REFINEMENT PHENIX 1.18.2-3874 INITIAL EULER ASSIGNMENT cryoSPARC 3.0 FINAL EULER ASSIGNMENT cryoSPARC 3.0 CLASSIFICATION cryoSPARC 3.0 RECONSTRUCTION cryoSPARC 3.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2974553