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AT from first module of the pikromycin synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QO3
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blotted for 3 seconds with a force of "1" before plunging.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 184737 Reported Resolution (Å) 2.86 Resolution Method FSC 0.143 CUT-OFF Other Details Maps were density modified using Phenix to a calculated resolution of 2.77 Angstroms. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (2QO3) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Phenix Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 70
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1500 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 61728 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Collected 4284 movies at 0 degrees tilt and 2912 movies at -30 degrees tilt
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 3.2.0 MODEL FITTING UCSF ChimeraX 1.1.1 MODEL FITTING PHENIX 1.19.2-4158 MODEL REFINEMENT Coot 0.8.9.2 MODEL REFINEMENT PHENIX 1.19.2-4158 INITIAL EULER ASSIGNMENT cryoSPARC 3.2.0 FINAL EULER ASSIGNMENT cryoSPARC 3.2.0 CLASSIFICATION cryoSPARC 3.2.0 RECONSTRUCTION cryoSPARC 3.2.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF correction performed by cryosparc during reconstruction 6761206 From blob picker, 6,761,206 particles were selected. Then, from template picker, 2,350,020 particles were selected.