1ZHN

Crystal Structure of mouse CD1d bound to the self ligand phosphatidylcholine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	100 mM Tris, 200 mM NH4(SO4)2, 25% PEG 4000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.798	α = 90
b = 106.909	β = 90
c = 110.06	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	IMAGE PLATE	MARRESEARCH		1998-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.0000	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	76.7	98.1	0.056	8.4	4.3	12734	12734		-3	39.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	96		0.29	2.5	4	1810

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1CD1	2.8	76.7	11481	11481	1018	98.15	0.22174	0.22174	0.21632	0.28097	RANDOM	25.724

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]
-1.34			-1.16		2.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.718
r_dihedral_angle_4_deg	23.189
r_dihedral_angle_3_deg	18.958
r_dihedral_angle_1_deg	7.16
r_scangle_it	1.722
r_angle_refined_deg	1.473
r_scbond_it	0.957
r_mcangle_it	0.773
r_angle_other_deg	0.766
r_mcbond_it	0.688
r_nbd_refined	0.209
r_symmetry_vdw_other	0.204
r_nbtor_refined	0.189
r_nbd_other	0.186
r_xyhbond_nbd_refined	0.178
r_symmetry_hbond_refined	0.17
r_symmetry_vdw_refined	0.11
r_nbtor_other	0.089
r_chiral_restr	0.078
r_mcbond_other	0.067
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2987
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	170

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling