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S. aureus YhaM D193A hexamer, D3 refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 3124511 Reported Resolution (Å) 2.36 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D3
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation coefficient (CCmask) Overall B Value 126.9 Fitting Procedure Details Model was built into main EM map de novo using ModelAngelo, then flexibly fit using PHENIX real-space model refinement.
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 47
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz 0.2.5 IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC 4.5.3 MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT cryoSPARC 4.5.3 FINAL EULER ASSIGNMENT cryoSPARC 4.5.3 CLASSIFICATION cryoSPARC 4.5.3 RECONSTRUCTION cryoSPARC 4.5.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 8389618