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Structure of zebrafish OTOP1 in nanodisc in complex with inhibitor C2.2
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 15.051 f_angle_d 0.97 f_chiral_restr 0.045 f_plane_restr 0.018 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 155580 Reported Resolution (Å) 3.23 Resolution Method FSC 0.143 CUT-OFF Other Details final reported resolution of 3.23A 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 K3 (6k x 4k) Electron Dose (electrons/Å**2) 49.9
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 600 Maximum Defocus (nm) 1800 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.4.1 IMAGE ACQUISITION Leginon CTF CORRECTION CTFFIND 4 MODEL FITTING Coot 0.9.8.7 INITIAL EULER ASSIGNMENT cryoSPARC 4.4.1 FINAL EULER ASSIGNMENT cryoSPARC 4.4.1 CLASSIFICATION cryoSPARC 4.4.1 RECONSTRUCTION cryoSPARC 4.4.1 MODEL REFINEMENT Coot 0.9.8.7 MODEL REFINEMENT PHENIX 1.20.1_4487 MODEL REFINEMENT Rosetta 2022.11
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 6147309