3HUJ

Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PO6PDB ENTRY 2po6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92910.1M Tris-HCl, 0.2M magnesium chloride, 12% PEG 10000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.7855.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.112α = 90
b = 82.36β = 101.26
c = 117.184γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97940APS23-ID-D

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
12.55091.10.0883660546605411
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)
12.52.5974.30.3441.72.75344

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2po62.547.2816242162421328890.520.219120.219120.215950.27883RANDOM42.503
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]
0.31-0.92-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.044
r_dihedral_angle_4_deg18.084
r_dihedral_angle_3_deg17.474
r_dihedral_angle_1_deg5.646
r_scangle_it1.246
r_angle_refined_deg1.119
r_scbond_it0.77
r_mcangle_it0.657
r_mcbond_it0.37
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.044
r_dihedral_angle_4_deg18.084
r_dihedral_angle_3_deg17.474
r_dihedral_angle_1_deg5.646
r_scangle_it1.246
r_angle_refined_deg1.119
r_scbond_it0.77
r_mcangle_it0.657
r_mcbond_it0.37
r_nbtor_refined0.3
r_symmetry_vdw_refined0.209
r_nbd_refined0.189
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.136
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12944
Nucleic Acid Atoms
Solvent Atoms482
Heterogen Atoms213

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling