2EYS | pdb_00002eys

A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MI5	PDB entry 1MI5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	297	9% PEG 3350, 0.1M cacodylate, 0.2M ammonium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.835	α = 90
b = 131.034	β = 90
c = 116.852	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 4		2005-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

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	2.21	65.51					22974

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1MI5	2.21	65.51	21787	1186	97.39	0.21756	0.21423	0.21065	0.25	0.27836	0.26	RANDOM	29.463

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]
-1.26			-0.52		1.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.122
r_dihedral_angle_4_deg	18.119
r_dihedral_angle_3_deg	17.998
r_dihedral_angle_1_deg	6.066
r_scangle_it	5.036
r_scbond_it	3.714
r_mcangle_it	2.405
r_mcbond_it	1.44
r_angle_refined_deg	1.25
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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	3527
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement