9EQ2 | pdb_00009eq2

Arabidopsis thaliana R2T complex


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d7.734
f_angle_d0.977
f_chiral_restr0.05
f_plane_restr0.007
f_bond_d0.006
Sample
AtR2T complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles185042
Reported Resolution (Å)3.68
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolBACKBONE TRACE
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)50.12
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0
CTF CORRECTIONCTFFIND4.1
MODEL FITTINGUCSF ChimeraX
INITIAL EULER ASSIGNMENTcryoSPARCv4.3.1
FINAL EULER ASSIGNMENTRELION4.0
CLASSIFICATIONRELION4.0
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTISOLDE1.7
MODEL REFINEMENTPHENIX1.20.1-4487
MODEL REFINEMENTCoot0.9.8.5
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2334954