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Cryo-EM structure of a Zinc-loaded wild-type YiiP-Fab complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KZZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.89 f_angle_d 0.536 f_chiral_restr 0.039 f_plane_restr 0.004 f_bond_d 0.003
Sample Wild-type Zinc-loaded YiiP-Fab complex
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 536206 Reported Resolution (Å) 3.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (7KZZ) Refinement Space REAL Refinement Protocol BACKBONE TRACE Refinement Target cross-correlation Overall B Value 200.5 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 FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 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 PARTICLE SELECTION cryoSPARC 3.1 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 3.1 MODEL FITTING UCSF Chimera 1.14 MODEL REFINEMENT PHENIX 1.18 INITIAL EULER ASSIGNMENT cryoSPARC 3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.1 CLASSIFICATION cryoSPARC 3.1 RECONSTRUCTION cryoSPARC 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3058414