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Structure of zebrafish OTOP1 in nanodisc in the presence of inhibitor C11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NF4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.643 f_angle_d 1.005 f_chiral_restr 0.094 f_plane_restr 0.019 f_bond_d 0.006
Sample zebrafish OTOP1 in MSP2N2 nanodisc
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 164766 Reported Resolution (Å) 3.73 Resolution Method FSC 0.143 CUT-OFF Other Details final reported resolution of 3.73A was obtained through the Remote 3DFSC Processing server Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (6NF4) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 50.37
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 800 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model OTHER Nominal Magnification 36000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3.0 IMAGE ACQUISITION Leginon CTF CORRECTION Gctf 1.06 MODEL FITTING Coot 0.9.8.7 MODEL REFINEMENT Coot 0.9.8.7 MODEL REFINEMENT PHENIX 1.20.1_4487 MODEL REFINEMENT Rosetta 2022.11 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.0 FINAL EULER ASSIGNMENT cryoSPARC 3.3.0 CLASSIFICATION cryoSPARC 3.3.0 RECONSTRUCTION cryoSPARC 3.3.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3410686