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Cryo-EM of the SLFN12-PDE3A complex: PDE3A body refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YD0
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.7824 f_angle_d 0.3677 f_chiral_restr 0.035 f_plane_restr 0.0035 f_bond_d 0.0018
Sample SLFN12-PDE3A complex, PDE3A body with interacting peptide from SLFN12
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 4.5 second blot time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 247402 Reported Resolution (Å) 2.97 Resolution Method FSC 0.143 CUT-OFF Other Details Multi-body refinement in Relion Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (5YD0) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details The atomic model (including per-residue ADP/B-factors) was refined in Phenix against the sharpened/local resolution-filtered map
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cisTEM 1.0.0-beta IMAGE ACQUISITION EPU 2.5 CTF CORRECTION CTFFIND 4.1.13 INITIAL EULER ASSIGNMENT cisTEM 1.0.0-beta FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 1.18 MODEL REFINEMENT Coot 0.8.9
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF correction was applied throughout the entire processing workflow, beginning with particle picking 2160426