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Cryo-EM structure of native SWR1 bound to DNA (composite structure)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GEJ in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.2799 f_angle_d 0.4908 f_chiral_restr 0.041 f_plane_restr 0.0034 f_bond_d 0.0032
Sample Native SWR1 bound to DNA. Sample Components Native SWR1 complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 6 second blot time and blot force of 12.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 101246 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refined maps were post-processed using DeepEMhancer Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6GEJ) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation coefficient Overall B Value 84 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 54
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 2000 Maximum Defocus (nm) 3600 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 48543 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1.3 IMAGE ACQUISITION SerialEM 3.7.6 CTF CORRECTION Gctf MODEL FITTING ISOLDE 1.7 INITIAL EULER ASSIGNMENT RELION 3.1.3 FINAL EULER ASSIGNMENT RELION 3.1.3 CLASSIFICATION RELION 3.1.3 RECONSTRUCTION RELION 3.1.3 MODEL REFINEMENT PHENIX 1.21_5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 386667 2D classification was used to remove graphene edges.