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Pfr conformer of Arabidopsis thaliana phytochrome B in complex with phytochrome-interacting factor 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P14713-F1 in silico model AlphaFold AF-Q8L5W7-F1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.515 f_angle_d 0.565 f_chiral_restr 0.039 f_plane_restr 0.004 f_bond_d 0.002
Sample Ternary complex of AtphyB-Pfr homodimer with AtPIF6 Sample Components complex of AtphyB-Pfr homodimer PIF6 monomer
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 325483 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2000 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 4.1.2 IMAGE ACQUISITION EPU 2.14 CTF CORRECTION cryoSPARC 4.1.2 MODEL FITTING UCSF ChimeraX 1.7.1 MODEL FITTING Coot 0.9.8.7 INITIAL EULER ASSIGNMENT RELION 4.0.0 FINAL EULER ASSIGNMENT cryoSPARC 4.1.2 CLASSIFICATION RELION 4.0.0 RECONSTRUCTION cryoSPARC 4.1.2 MODEL REFINEMENT PHENIX 1.20
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION