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Structure of C-terminal LRRK2 bound to MLi-2 (I2020T mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VP7
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.907 f_angle_d 0.6 f_chiral_restr 0.043 f_plane_restr 0.005 f_bond_d 0.002
Sample C-terminal LRRK2 (I2020T mutation) bound to MLi-2
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot force = 3
Blot time = 4 seconds
Wait time = 20 seconds
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 380487 Reported Resolution (Å) 2.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D2
Map-Model Fitting and Refinement Id 1 (6VP7) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 55
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 4000 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 Topaz 0.2.5 IMAGE ACQUISITION cryoSPARC 4.0 CTF CORRECTION CTFFIND 4.0 MODEL FITTING UCSF ChimeraX 1.5 MODEL REFINEMENT PHENIX 1.20 INITIAL EULER ASSIGNMENT cryoSPARC 4.0 FINAL EULER ASSIGNMENT cryoSPARC 4.0 RECONSTRUCTION cryoSPARC 4.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 628666