2AKR

Structural basis of sulfatide presentation by mouse CD1d

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z5L	PDB ENTRY 1Z5L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	277	ammonium sulfate, NaCl, sodium cacodylate, manganese chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.858	α = 90
b = 74.843	β = 102.1
c = 101.564	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	ADSC QUANTUM 315		2005-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	1.9	50	98.7	0.089	15.9	2.4		67171			19.8

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	1.9	1.97	99.7		0.58	2.4

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1Z5L	1.9	41.38	67104	65745	1359	98.6	0.187	0.186	0.249	RANDOM	27.481

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.604
r_dihedral_angle_4_deg	22.316
r_dihedral_angle_3_deg	16.911
r_dihedral_angle_1_deg	6.409
r_scangle_it	3.771
r_scbond_it	2.524
r_angle_refined_deg	1.749
r_mcangle_it	1.517
r_mcbond_it	1.012
r_nbtor_refined	0.311
r_symmetry_hbond_refined	0.283
r_nbd_refined	0.215
r_symmetry_vdw_refined	0.213
r_xyhbond_nbd_refined	0.2
r_chiral_restr	0.141
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
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	5950
Nucleic Acid Atoms
Solvent Atoms	748
Heterogen Atoms	220

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
CCP4	data scaling
MOLREP	phasing