3SDX

Crystal structure of human autoreactive-Valpha24 NKT TCR in complex with CD1d-beta-galactosylceramide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	30% PEG 400, 0.1M Tris, 0.1M MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.58	65.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.041	α = 90
b = 152.337	β = 97.24
c = 85.119	γ = 90

Symmetry
Space Group	C 1 2 1

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	mirrors	2011-03-10		SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.12	122.77	100				46742	1	1	60.377

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	3.12	122.77	46742	2362	99.04	0.234	0.2319	0.273	RANDOM	61.5591

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]
1.87		-3.24	-3.77		1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.037
r_dihedral_angle_3_deg	19.999
r_dihedral_angle_4_deg	18.784
r_dihedral_angle_1_deg	6.007
r_scangle_it	1.962
r_angle_refined_deg	1.271
r_mcangle_it	1.183
r_scbond_it	1.079
r_mcbond_it	0.628
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.037
r_dihedral_angle_3_deg	19.999
r_dihedral_angle_4_deg	18.784
r_dihedral_angle_1_deg	6.007
r_scangle_it	1.962
r_angle_refined_deg	1.271
r_mcangle_it	1.183
r_scbond_it	1.079
r_mcbond_it	0.628
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12668
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	90

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.