2PO6

Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EYSPDB entry 2EYS followed by PDB entry 1ZT4 (without alpha-Galcer)
experimental modelPDB 1ZT4PDB entry 2EYS followed by PDB entry 1ZT4 (without alpha-Galcer)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529813% PEG 10K, 0.1M bis-tris propane, 0.2M tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.6266.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 204.012α = 90
b = 155.636β = 94.78
c = 85.981γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDADSC QUANTUM 2102007-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.23095.30.1386.43.142581
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.3174.70.4861.83310

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2EYS followed by PDB entry 1ZT4 (without alpha-Galcer)3.229.1842133213595.580.2290.2260.293RANDOM57.718
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]
0.18-0.14-0.01-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.069
r_dihedral_angle_3_deg19.437
r_dihedral_angle_4_deg17.605
r_dihedral_angle_1_deg5.984
r_angle_refined_deg1.151
r_scangle_it0.833
r_scbond_it0.476
r_mcangle_it0.396
r_nbtor_refined0.303
r_mcbond_it0.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.069
r_dihedral_angle_3_deg19.437
r_dihedral_angle_4_deg17.605
r_dihedral_angle_1_deg5.984
r_angle_refined_deg1.151
r_scangle_it0.833
r_scbond_it0.476
r_mcangle_it0.396
r_nbtor_refined0.303
r_mcbond_it0.216
r_nbd_refined0.198
r_symmetry_vdw_refined0.182
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.148
r_chiral_restr0.085
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13083
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms215

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction
MOLREPphasing