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Cryo-EM structure of the zebrafish TRPM2 channel in the apo conformation, processed with C2 symmetry (pseudo C4 symmetry)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D73
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.714 f_angle_d 0.951 f_chiral_restr 0.052 f_bond_d 0.007 f_plane_restr 0.007
Sample Transient receptor potential cation channel subfamily M member 2
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 58005 Reported Resolution (Å) 4.5 Resolution Method FSC 0.143 CUT-OFF Other Details No symmetry (C1) was imposed during reconstructions and classifications. C2 symmetry was imposed during the final 3D auto-refinement. Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (6D73) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 100 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 750 Maximum Defocus (nm) 2500 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 22500 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.0 IMAGE ACQUISITION Latitude CTF CORRECTION RELION 3.0 CTF CORRECTION Gctf 1.18 MODEL FITTING Coot 0.8.8 INITIAL EULER ASSIGNMENT RELION 3.0 FINAL EULER ASSIGNMENT RELION 3.0 RECONSTRUCTION RELION 3.0 MODEL REFINEMENT PHENIX 1.12-2829
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 301199