6DFX

human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27810% PEG 8000, 100mM cacodylate pH6.2, 400mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.9257.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.705α = 90
b = 88.896β = 104.26
c = 116.777γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979100APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.035098.114.44.5142449
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.032.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.0350.01135207724199.230.182730.180830.21657RANDOM49.024
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]
-0.61.090.5-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.424
r_dihedral_angle_3_deg17.622
r_dihedral_angle_4_deg17.346
r_dihedral_angle_1_deg8.284
r_long_range_B_refined5.89
r_long_range_B_other5.89
r_scangle_other4.412
r_mcangle_it3.109
r_mcangle_other3.109
r_scbond_it2.961
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.424
r_dihedral_angle_3_deg17.622
r_dihedral_angle_4_deg17.346
r_dihedral_angle_1_deg8.284
r_long_range_B_refined5.89
r_long_range_B_other5.89
r_scangle_other4.412
r_mcangle_it3.109
r_mcangle_other3.109
r_scbond_it2.961
r_scbond_other2.96
r_angle_refined_deg2.493
r_mcbond_it2.14
r_mcbond_other2.14
r_angle_other_deg1.796
r_chiral_restr0.158
r_bond_refined_d0.028
r_gen_planes_refined0.014
r_bond_other_d0.009
r_gen_planes_other0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12872
Nucleic Acid Atoms
Solvent Atoms775
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing