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Inducible lysine decarboxylase LdcI stacks, pH 5.7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N75
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.8374 f_angle_d 0.9218 f_chiral_restr 0.0573 f_plane_restr 0.0065 f_bond_d 0.0062
Sample E. coli inducible lysine decarboxylase at pH 5.7
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 15157 Reported Resolution (Å) 3.28 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D5
Map-Model Fitting and Refinement Id 1 (3N75) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value 96 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 29.3
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 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 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4 CTF CORRECTION Gctf MODEL FITTING UCSF Chimera MODEL REFINEMENT PHENIX 1.13 INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 15165