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ytrEF nucleotide-free conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Sample Bacillus ABC transporter ytrEF in nucleotide-free conformation
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 137371 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Refinement in phenix.real_space_refine
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 44.34
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 700 Maximum Defocus (nm) 1800 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.4.1 CTF CORRECTION cryoSPARC 4.4.1 MODEL FITTING UCSF Chimera 1.16 INITIAL EULER ASSIGNMENT cryoSPARC 4.4.1 FINAL EULER ASSIGNMENT cryoSPARC 4.4.1 CLASSIFICATION RELION 5.0 RECONSTRUCTION cryoSPARC 4.4.1 MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF estimation was performed in cryoSPARC. 8685623