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Human meprin alpha inhibitory complex with compound 10d (N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GWN
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.455 f_angle_d 1.801 f_chiral_restr 0.104 f_plane_restr 0.02 f_bond_d 0.012
Sample Tetrameric portion of helical meprin alpha in complex with a small molecule inhibitor
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 s blot, -3 force
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 235162 Reported Resolution (Å) 2.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4GWN) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 44.5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1200 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 crYOLO 1.8.1 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1.13 CTF CORRECTION Warp 1.0.7 MODEL FITTING ISOLDE 1.1.0 MODEL FITTING UCSF ChimeraX 1.3 MODEL FITTING Coot 0.9.2 MODEL REFINEMENT ISOLDE 1.1.0 MODEL REFINEMENT PHENIX 1.17 INITIAL EULER ASSIGNMENT RELION 2.1, 3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 925458 Subparticles extracted after particle expansion about pseudo-helical symmetry