Experiment: 9RSE

Human 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	8.2	293.15	12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate, 0.1 M bicine/Trizma base pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.6218	α = 90
b = 156.3734	β = 90
c = 51.9093	γ = 90

Symmetry
Space Group	P 21 21 2

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 PILATUS 6M		2021-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9253	ESRF	ID30B

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	1.76	49.27	96.62	0.094	0.049	0.968	14.8	3.3		92489			24.95

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	1.76	1.79	71.07		0.937	0.487	0.532	1.1	3.1

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	1.76	49.266	92323	2016	96.44	0.2132	0.2121	0.2542	0.254	35.42

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]
4.77060556			-1.06836745		-3.70223811

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	15.1817
s_dihedral_angle_3_deg	11.7448
s_dihedral_angle_1_deg	7.3264
s_dihedral_angle_2_deg	4.9407
s_angle_nonh_deg	2.0822
s_nbtor	0.2238
s_nbd	0.2216
s_symmetry_nbd	0.2151
s_symmetry_hbond_nbd	0.1926
s_hbond_nbd	0.182

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	15.1817
s_dihedral_angle_3_deg	11.7448
s_dihedral_angle_1_deg	7.3264
s_dihedral_angle_2_deg	4.9407
s_angle_nonh_deg	2.0822
s_nbtor	0.2238
s_nbd	0.2216
s_symmetry_nbd	0.2151
s_symmetry_hbond_nbd	0.1926
s_hbond_nbd	0.182
s_chiral_restr	0.0938
s_planes	0.0152
s_bond_nonh_d	0.0132

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6028
Nucleic Acid Atoms
Solvent Atoms	699
Heterogen Atoms	152

Software

Software
Software Name	Purpose
xia2	data scaling
DIALS	data reduction
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.