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Cryo-EM structure of the inward-facing apo NhaA in the unplugged state at pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9RH1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.171 f_angle_d 0.718 f_chiral_restr 0.044 f_bond_d 0.004 f_plane_restr 0.004
Sample NhaA in complex with Fv6F9 Sample Components NhaA Fv6F9
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 92700 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 (9RH1) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1100 Maximum Defocus (nm) 2100 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz 0.2.5a IMAGE ACQUISITION EPU 3.6 CTF CORRECTION RELION 4 MODEL FITTING ISOLDE MODEL FITTING Coot 0.9.8 INITIAL EULER ASSIGNMENT RELION 4 FINAL EULER ASSIGNMENT RELION 4 CLASSIFICATION RELION 4 RECONSTRUCTION RELION 4 MODEL REFINEMENT PHENIX 1.20.1_4487:
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION