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PSI complex of A.thaliana isolated using DOC based Clear-Native-PAGE method
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8J7B
Refinement RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 15.1713 s_dihedral_angle_3_deg 12.0455 s_dihedral_angle_1_deg 6.5315 s_dihedral_angle_2_deg 3.5484 s_angle_nonh_deg 2.0721 s_nbtor 0.2373 s_nbd 0.2201 s_hbond_nbd 0.1612 s_chiral_restr 0.0999 s_bond_nonh_d 0.0196
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 15.1713 s_dihedral_angle_3_deg 12.0455 s_dihedral_angle_1_deg 6.5315 s_dihedral_angle_2_deg 3.5484 s_angle_nonh_deg 2.0721 s_nbtor 0.2373 s_nbd 0.2201 s_hbond_nbd 0.1612 s_chiral_restr 0.0999 s_bond_nonh_d 0.0196 s_planes 0.0106
Sample PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method
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 148985 Reported Resolution (Å) 2.18 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8J7B) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 40.0832 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.01 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 Topaz CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF ChimeraX 1.9 MODEL FITTING Coot 0.9.8.7 INITIAL EULER ASSIGNMENT RELION 4.0.2 FINAL EULER ASSIGNMENT RELION 4.0.2 CLASSIFICATION RELION 4.0.2 RECONSTRUCTION RELION 4.0.2 MODEL REFINEMENT Servalcat 0.4.115
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 1629453