3T1F

Crystal structure of the mouse CD1d-Glc-DAG-s2 complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52778% tacsimate pH 7.5, 17% PEG3350 , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8256.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.191α = 90
b = 107.381β = 90
c = 110.305γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.9795SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.74298.80.04625.53.95683956157
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7697.10.5362.23.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.74253747172398.80.18780.186780.2192RANDOM27.648
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]
-0.87-1.091.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.692
r_dihedral_angle_4_deg23.414
r_dihedral_angle_3_deg13.391
r_dihedral_angle_1_deg6.114
r_scangle_it3.381
r_scbond_it2.191
r_angle_refined_deg1.489
r_mcangle_it1.369
r_mcbond_it0.777
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.692
r_dihedral_angle_4_deg23.414
r_dihedral_angle_3_deg13.391
r_dihedral_angle_1_deg6.114
r_scangle_it3.381
r_scbond_it2.191
r_angle_refined_deg1.489
r_mcangle_it1.369
r_mcbond_it0.777
r_chiral_restr0.104
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 AtomsNumber
Protein Atoms2895
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms139

Software

Software
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling