9IUZ

Constitutively active mutant(Y276H) of Arabidopsis phytochrome B(phyB) in complex with phytochrome-interacting factor 6(PIF6)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-P14713-F1 
in silico modelAlphaFoldAF-Q8L5W7-F1 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.747
f_angle_d0.518
f_chiral_restr0.039
f_plane_restr0.004
f_bond_d0.002
Sample
Ternary complex of phyB mutant(Y276H) with PIF6
Sample Components
complex of phyB mutant(Y276H) homodimer
PIF6 monomer
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles366884
Reported Resolution (Å)3.19
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (8YB4, 8YB4, 8YB4)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.1.2
IMAGE ACQUISITIONEPU2.14
CTF CORRECTIONcryoSPARC4.1.2
MODEL FITTINGUCSF ChimeraX1.7.1
MODEL FITTINGCoot0.9.8.7
INITIAL EULER ASSIGNMENTcryoSPARC4.1.2
FINAL EULER ASSIGNMENTcryoSPARC4.1.2
CLASSIFICATIONcryoSPARC4.1.2
RECONSTRUCTIONcryoSPARC4.1.2
MODEL REFINEMENTPHENIX1.20
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION