3RZC | pdb_00003rzc

Structure of the self-antigen iGb3 bound to mouse CD1d and in complex with the iNKT TCR

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	300	16% polyethylene glycol 3350, 8% tacsimate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.103	α = 90
b = 191.346	β = 90
c = 151.032	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	MARMOSAIC 325 mm CCD		2011-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.979	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	2.8	50	98.9	0.137	12.7	4	28702	28387

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	2.8	2.87	99.9		0.695	2.2	4	1894

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	49.65	26949	1438	98.87	0.23729	0.23555	0.2315	0.27054	0.2643	RANDOM	46.528

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]
-0.05			0.09		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.344
r_dihedral_angle_3_deg	12.049
r_dihedral_angle_4_deg	11.812
r_dihedral_angle_1_deg	4.144
r_angle_refined_deg	0.835
r_scangle_it	0.341
r_scbond_it	0.184
r_mcangle_it	0.145
r_mcbond_it	0.076
r_chiral_restr	0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.344
r_dihedral_angle_3_deg	12.049
r_dihedral_angle_4_deg	11.812
r_dihedral_angle_1_deg	4.144
r_angle_refined_deg	0.835
r_scangle_it	0.341
r_scbond_it	0.184
r_mcangle_it	0.145
r_mcbond_it	0.076
r_chiral_restr	0.047
r_bond_refined_d	0.005
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6360
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	186

Software

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