2PO6 | pdb_00002po6

Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EYS	PDB entry 2EYS followed by PDB entry 1ZT4 (without alpha-Galcer)
experimental model	PDB	1ZT4	PDB entry 2EYS followed by PDB entry 1ZT4 (without alpha-Galcer)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	13% PEG 10K, 0.1M bis-tris propane, 0.2M tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.62	66.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 204.012	α = 90
b = 155.636	β = 94.78
c = 85.981	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	113	CCD	ADSC QUANTUM 210		2007-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1	APS	17-ID

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	3.2	30	95.3	0.138	6.4	3.1		42581

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	3.2	3.31	74.7		0.486		1.8	3310

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2EYS followed by PDB entry 1ZT4 (without alpha-Galcer)	3.2	29.18	42133	2135	95.58	0.229	0.226	0.2174	0.293	0.2783	RANDOM	57.718

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]
0.18		-0.14	-0.01		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.069
r_dihedral_angle_3_deg	19.437
r_dihedral_angle_4_deg	17.605
r_dihedral_angle_1_deg	5.984
r_angle_refined_deg	1.151
r_scangle_it	0.833
r_scbond_it	0.476
r_mcangle_it	0.396
r_nbtor_refined	0.303
r_mcbond_it	0.216

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.069
r_dihedral_angle_3_deg	19.437
r_dihedral_angle_4_deg	17.605
r_dihedral_angle_1_deg	5.984
r_angle_refined_deg	1.151
r_scangle_it	0.833
r_scbond_it	0.476
r_mcangle_it	0.396
r_nbtor_refined	0.303
r_mcbond_it	0.216
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.182
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.085
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13083
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	215

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
MOLREP	phasing

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.