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Cryo-EM structure of violaxanthin-chlorophyll-a-binding protein with red shifted Chl a (rVCP) from Trachydiscus minutus at 2.4 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RWT
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.98 f_angle_d 1.176 f_chiral_restr 0.058 f_bond_d 0.011 f_plane_restr 0.007
Sample Tetrameric light-harvesting complex from Trachydiscus minutus.
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 290174 Reported Resolution (Å) 2.42 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (1RWT) 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) 80
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 Minimum Defocus (nm) 700 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model JEOL CRYOSPECPORTER Nominal Magnification 60000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.2.1 IMAGE ACQUISITION SerialEM 4.1.0beta CTF CORRECTION cryoSPARC 4.2.1 MODEL FITTING UCSF Chimera 1.17.1 MODEL REFINEMENT Coot 0.9.4.1 MODEL REFINEMENT PHENIX 1.19.2 INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1 FINAL EULER ASSIGNMENT cryoSPARC 4.2.1 RECONSTRUCTION cryoSPARC 4.2.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 6610197