3HUJ

Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PO6	PDB ENTRY 2po6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	291	0.1M Tris-HCl, 0.2M magnesium chloride, 12% PEG 10000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.112	α = 90
b = 82.36	β = 101.26
c = 117.184	γ = 90

Symmetry
Space Group	P 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	100	CCD	MARMOSAIC 300 mm CCD		2008-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97940	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	50	91.1	0.088		3	66054	66054	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	74.3		0.344	1.7	2.7	5344

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2po6	2.5	47.28	1	62421	62421	3288	90.52	0.21912	0.21912	0.21595	0.27883	RANDOM	42.503

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]
0.31		-0.92			-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.044
r_dihedral_angle_4_deg	18.084
r_dihedral_angle_3_deg	17.474
r_dihedral_angle_1_deg	5.646
r_scangle_it	1.246
r_angle_refined_deg	1.119
r_scbond_it	0.77
r_mcangle_it	0.657
r_mcbond_it	0.37
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.044
r_dihedral_angle_4_deg	18.084
r_dihedral_angle_3_deg	17.474
r_dihedral_angle_1_deg	5.646
r_scangle_it	1.246
r_angle_refined_deg	1.119
r_scbond_it	0.77
r_mcangle_it	0.657
r_mcbond_it	0.37
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.209
r_nbd_refined	0.189
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.136
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12944
Nucleic Acid Atoms
Solvent Atoms	482
Heterogen Atoms	213

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.