3HE7 | pdb_00003he7

Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta7 NKT TCR

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	17% polyethylene glycol 10K, 0.1M ammonium acetate, 0.1M Bis Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3	58.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.229	α = 90
b = 81.913	β = 90
c = 243.253	γ = 90

Symmetry
Space Group	P 21 21 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 210		2008-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95667	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	99.7	0.132	0.132	13.7	7	29526	29526	1	1	61.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	99.1		0.707	0.707	2.2	5.8	4192

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	3HE6	2.8	50	1	1	28041	28041	1480	99.65	0.22614	0.22368	0.25	0.27117	0.29	RANDOM	44.162

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]
0.95			0.74		-1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.532
r_dihedral_angle_3_deg	16.983
r_dihedral_angle_4_deg	16.185
r_dihedral_angle_1_deg	5.476
r_angle_refined_deg	1.029
r_scangle_it	0.914
r_scbond_it	0.545
r_mcangle_it	0.403
r_nbtor_refined	0.299
r_mcbond_it	0.229

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.532
r_dihedral_angle_3_deg	16.983
r_dihedral_angle_4_deg	16.185
r_dihedral_angle_1_deg	5.476
r_angle_refined_deg	1.029
r_scangle_it	0.914
r_scbond_it	0.545
r_mcangle_it	0.403
r_nbtor_refined	0.299
r_mcbond_it	0.229
r_nbd_refined	0.184
r_symmetry_vdw_refined	0.145
r_symmetry_hbond_refined	0.12
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6528
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	116

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.