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PLD-fold vaccinia virus endonuclease K4 with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 30IE
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.5337 f_angle_d 0.4813 f_chiral_restr 0.0456 f_plane_restr 0.0035 f_bond_d 0.0032
Sample Octameric complex of K4 containing mutated histidines in the HKD motif, with DNA bound in chains A and D
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 23730 Reported Resolution (Å) 2.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (30IE) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target cross-correlation coefficient Overall B Value 133.56 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 42
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model 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 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4 MODEL FITTING UCSF ChimeraX MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC 4 FINAL EULER ASSIGNMENT cryoSPARC 4 CLASSIFICATION cryoSPARC 4 RECONSTRUCTION cryoSPARC 4 MODEL REFINEMENT PHENIX 2.0_5936
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION