3SDA

Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-galactosylceramide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	293	0.1M Sodium Citrate, 15% PEG 6000, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.75	α = 90
b = 94.75	β = 90
c = 287.52	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	213	CCD	ADSC QUANTUM 315r		2011-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	1.47	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.8	67.38	100	0.183	0.183	6.4	6	32322	32322	1	1	76.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	65.25	32297	1634	97.01	0.2738	0.2718	0.31221	RANDOM	59.6

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]
0.14			0.14		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.505
r_dihedral_angle_4_deg	23.635
r_dihedral_angle_3_deg	19.508
r_dihedral_angle_1_deg	6.189
r_angle_refined_deg	1.982
r_mcangle_it	1.864
r_mcbond_it	1.51
r_scangle_it	1.051
r_scbond_it	0.583
r_chiral_restr	0.13
r_bond_refined_d	0.045
r_gen_planes_refined	0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6558
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	119

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling