Experiment: 9RSF

Macaque CD1d with lipid antigen bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	10% w/v PEG 8000, 20% v/v ethylene glycol 0.03 M, 0.1 M MES/imidazole pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.0613	α = 90
b = 87.0613	β = 90
c = 232.805	γ = 120

Symmetry
Space Group	P 32 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	100	PIXEL	DECTRIS EIGER2 XE 16M		2022-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.83	54.08	98.22	0.056	0.013	1	32.7	17.1		89434			24.77

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.86	84.73		0.486	0.179	0.914	2.1	6.7

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.83	54.076	89349	2075	98.12	0.171	0.1707	0.2171	0.2161	33.15

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]
2.81595458			2.81595458		-5.63190917

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	15.2774
s_dihedral_angle_3_deg	12.2411
s_dihedral_angle_1_deg	7.2225
s_dihedral_angle_2_deg	3.0335
s_angle_nonh_deg	2.0335
s_nbtor	0.2246
s_nbd	0.2141
s_symmetry_hbond_nbd	0.1974
s_symmetry_nbd	0.1928
s_hbond_nbd	0.1671

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	15.2774
s_dihedral_angle_3_deg	12.2411
s_dihedral_angle_1_deg	7.2225
s_dihedral_angle_2_deg	3.0335
s_angle_nonh_deg	2.0335
s_nbtor	0.2246
s_nbd	0.2141
s_symmetry_hbond_nbd	0.1974
s_symmetry_nbd	0.1928
s_hbond_nbd	0.1671
s_chiral_restr	0.0977
s_planes	0.0153
s_bond_nonh_d	0.0137

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6056
Nucleic Acid Atoms
Solvent Atoms	1070
Heterogen Atoms	151

Software

Software
Software Name	Purpose
DIALS	data reduction
xia2	data scaling
gemmi	data extraction
MOLREP	phasing
Coot	model building
Servalcat	refinement

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.