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CryoEM structure of an inward-facing MelBSt at a Na(+)-bound and sugar low-affinity conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L17 in silico model AlphaFold experimental model PDB 7PHP
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.0701 f_angle_d 0.4978 f_chiral_restr 0.0398 f_bond_d 0.0028 f_plane_restr 0.0028
Sample MelBSt bound with Nb725_4-NabFab complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK II Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 296925 Reported Resolution (Å) 3.29 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7L17, 7PHP, 7PHP) Refinement Space Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI CETA (4k x 4k) Electron Dose (electrons/Å**2) 1.28
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v3 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC v3 MODEL FITTING UCSF ChimeraX MODEL FITTING PHENIX MODEL REFINEMENT PHENIX 1.20 CLASSIFICATION cryoSPARC v4 RECONSTRUCTION cryoSPARC cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION using cryoSPARC patch CTF estimation