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High-resolution cryo-EM structure of KdpFABC in the E1P-ADP state in lipid nanodisc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LC3
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.027 f_angle_d 0.476 f_chiral_restr 0.035 f_bond_d 0.003 f_plane_restr 0.003
Sample KdpFABC complex in the E1P-ADP state in lipid 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 672405 Reported Resolution (Å) 2.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7LC3) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target cross-correlation Overall B Value 59.2 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 2200 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.6.0 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 4.6.0 MODEL FITTING UCSF Chimera 1.14 MODEL FITTING Coot 0.9.8.95 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.0 FINAL EULER ASSIGNMENT cryoSPARC 4.6.0 CLASSIFICATION cryoSPARC 4.6.0 RECONSTRUCTION cryoSPARC 4.6.0 MODEL REFINEMENT PHENIX 1.18
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 10282000