☰ Navigation Tabs
Structure of a DNA-loaded MCM double hexamer engaged with the Dbf4-dependent kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F0L experimental model PDB 5BK4 experimental model PDB 6EYC experimental model PDB 6YA7 experimental model PDB 3QBZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.3356 f_angle_d 0.5389 f_chiral_restr 0.0417 f_plane_restr 0.0041 f_bond_d 0.0025
Sample DNA-loaded MCM double hexamer engaged with the dimeric Dbf4-dependent kinase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blotted for 3 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 149876 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6F0L, 5BK4, 6EYC, 6YA7, 3QBZ) Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 51.3
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 2000 Maximum Defocus (nm) 4100 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.40 IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.06 MODEL FITTING UCSF Chimera 1.14 MODEL REFINEMENT PHENIX 1.19.2 INITIAL EULER ASSIGNMENT cryoSPARC 2.8 FINAL EULER ASSIGNMENT RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION