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Tra1 subunit from Saccharomyces cerevisiae SAGA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OJS
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.638 f_angle_d 1.02 f_chiral_restr 0.051 f_plane_restr 0.009 f_bond_d 0.007
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot for 4 seconds and wait for 30 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 176464 Reported Resolution (Å) 4.6 Resolution Method FSC 0.143 CUT-OFF Other Details GPU accelerated Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5OJS) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 5.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.1 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 81000 Calibrated Magnification 81000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Gautomatch 0.56 CTF CORRECTION Gctf 1.06 MODEL FITTING PHENIX 1.13 MODEL REFINEMENT PHENIX 1.13 INITIAL EULER ASSIGNMENT cryoSPARC 1.6 FINAL EULER ASSIGNMENT RELION 2.0 CLASSIFICATION RELION 2.0 RECONSTRUCTION RELION 2.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE GPU accelerated 1350000 GPU accelerated