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Cryo-EM Structure of KdpFABC in E2-P state with BeF3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MRW
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.422 f_angle_d 1.088 f_chiral_restr 0.058 f_bond_d 0.009 f_plane_restr 0.008
Sample KdpFABC in E2-P intermediate state with BeF3
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 uL of protein mixture applied to grid. Blot time 4 seconds, blot force 0, no wait before plunging.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 223443 Reported Resolution (Å) 3.7 Resolution Method FSC 0.143 CUT-OFF Other Details non-uniform refinement Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5MRW) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 2.9.0 MODEL FITTING UCSF Chimera 1.13 INITIAL EULER ASSIGNMENT cryoSPARC 2.9.0 FINAL EULER ASSIGNMENT cryoSPARC 2.9.0 CLASSIFICATION cryoSPARC 2.9.0 RECONSTRUCTION cryoSPARC 2.9.0 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 1525715 template based picking