3O8X | pdb_00003o8x

Recognition of Glycolipid Antigen by iNKT Cell TCR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q7Y	2Q7Y, 3HE6
experimental model	PDB	3HE6	2Q7Y, 3HE6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	295	18% polyethylene glycol 3350, 0.2 M ammonium citrate dibasic, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79	α = 90
b = 191.2	β = 90
c = 151.2	γ = 90

Symmetry
Space Group	C 2 2 21

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	ADSC QUANTUM 315r	Rh coated flat mirror; single crystal	2010-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97946	SSRL	BL7-1

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	2.74	50	95.9	0.05	15.3	5.6	30526	29275			58.58

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)
	2.74	2.84	97.5		0.464	2.68	5.5	2921

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2Q7Y, 3HE6	2.74	41.47	27778	1493	95.7	0.19797	0.19495	0.25271	0.2165	RANDOM	41.065

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]
-0.03			-0.02		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.062
r_dihedral_angle_3_deg	17.747
r_dihedral_angle_4_deg	15.296
r_dihedral_angle_1_deg	6.444
r_scangle_it	2.76
r_scbond_it	1.668
r_angle_refined_deg	1.43
r_mcangle_it	1.056
r_mcbond_it	0.526
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6360
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	128

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling