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Structure of TRPV1 determined in lipid nanodisc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3J5P
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.837 f_angle_d 0.913 f_chiral_restr 0.056 f_bond_d 0.008 f_plane_restr 0.005
Sample TRPV1 ion channel in unliganded state
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 30689 Reported Resolution (Å) 3.28 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C4
Map-Model Fitting and Refinement Id 1 (3J5P) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 41
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI POLARA 300 Minimum Defocus (nm) 700 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2 Imaging Mode BRIGHT FIELD Specimen Holder Model OTHER Nominal Magnification 31000 Calibrated Magnification 41132 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Grid screening was performed manually.
EM Software Task Software Package Version PARTICLE SELECTION SPIDER IMAGE ACQUISITION UCSFImage4 CTF CORRECTION CTFFIND4 4 MODEL FITTING UCSF Chimera 1.10 INITIAL EULER ASSIGNMENT RELION 1.3 FINAL EULER ASSIGNMENT RELION 1.3 CLASSIFICATION RELION 1.3 RECONSTRUCTION RELION 1.3 MODEL REFINEMENT Coot MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF correction was performed before classification and refinement. 159193 Initial manual particle picking and automatic particle picking were performed using SamViewer and several python scripts based on SPIDER.