3SDC

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	293	13.5% PEG 6000, 0.1M Sodium citrate, pH 6.1, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.35	α = 90
b = 94.35	β = 90
c = 287.86	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	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)	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	3.1	89.657	98.4	0.222	6.9	5.6	23961	23961

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.27	99.1		0.01	1.028	1.124	0.447	0.8	6	3451

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	3.1	66.72	23951	1225	97.52	0.2429	0.2402	0.2921	RANDOM	62.6847

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]
-0.62			-0.62		1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.241
r_dihedral_angle_4_deg	17.438
r_dihedral_angle_3_deg	17.292
r_dihedral_angle_1_deg	6.213
r_scangle_it	1.38
r_angle_refined_deg	1.209
r_mcangle_it	0.801
r_scbond_it	0.753
r_mcbond_it	0.429
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.241
r_dihedral_angle_4_deg	17.438
r_dihedral_angle_3_deg	17.292
r_dihedral_angle_1_deg	6.213
r_scangle_it	1.38
r_angle_refined_deg	1.209
r_mcangle_it	0.801
r_scbond_it	0.753
r_mcbond_it	0.429
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6516
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	137

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
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.