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Structure of the DNase I- and phalloidin-bound pointed end of F-actin (conformer 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T20 experimental model PDB 2A42
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.771 f_angle_d 0.564 f_chiral_restr 0.044 f_plane_restr 0.003 f_bond_d 0.002
Sample F-actin pointed end bound by DNase I and phalloidin. Sample Components Actin filament pointed end Phalloidin Two DNase I molecules, each bound to the ultimate and penultimate actin subunits of the F-actin pointed end.
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details 3 seconds, force 0.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 161657 Reported Resolution (Å) 3.84 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6T20, 2A42) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details Real Space Refinement in Phenix.
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 64.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.01 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector.
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.8 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.13 MODEL FITTING UCSF ChimeraX 1.6.1 MODEL FITTING Coot 0.9.8.1 INITIAL EULER ASSIGNMENT cryoSPARC v3.3.2 FINAL EULER ASSIGNMENT cryoSPARC v4.2.1 CLASSIFICATION cryoSPARC v4.2.1 RECONSTRUCTION cryoSPARC v4.2.1 MODEL REFINEMENT Coot 0.9.8.1 MODEL REFINEMENT PHENIX 1.21rc1_5015
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4418492 Particles picked using SPHIRE-crYOLO.