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Single particle cryo-EM structure of MdtF V610F with bound Rhodamine 6G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QPS
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.5935 f_angle_d 0.5208 f_chiral_restr 0.0399 f_plane_restr 0.0043 f_bond_d 0.0028
Sample R6G-bound homotrimer of V610F multidrug resistance protein MdtF in SMALP nanodisc
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 1967418 Reported Resolution (Å) 3.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (9QPS) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 41.25
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 150000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 4.0 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.0 MODEL FITTING Coot MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT RELION 4.0 FINAL EULER ASSIGNMENT RELION 4.0 CLASSIFICATION RELION 4.0 RECONSTRUCTION RELION 4.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4498131