7BEQ

MicroED structure of the MyD88 TIR domain higher-order assembly


ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4W8G 

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.06α = 90
b = 31.01β = 107.696
c = 54.3γ = 90
Symmetry
Space GroupC 1 2 1

Data Collection

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
ELECTRON CRYSTALLOGRAPHYMOLECULAR REPLACEMENTTHROUGHOUT4W8G330.541.36243612973.840.22610.22290.2852.01
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.9175
f_angle_d0.5243
f_chiral_restr0.0425
f_plane_restr0.0037
f_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1133
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
PHASERphasing
Sample
Myeloid differentiation primary response protein MyD88
Specimen Preparation
Sample Aggregation State3D ARRAY
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodCRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)
Resolution MethodDIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type3D CRYSTAL
Space Group Name
Length a99.06
Length b31.01
Length c31.01
Angle Alpha90
Angle Beta107.7
Angle Gamma90
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeOTHER
Electron Dose (electrons/Å**2)0.08
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelJEOL 2100
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeDIFFRACTION
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceLAB6
Acceleration Voltage (kV)200
Imaging Details
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE