2EYS

A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MI5PDB entry 1MI5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.42979% PEG 3350, 0.1M cacodylate, 0.2M ammonium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.244.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.835α = 90
b = 131.034β = 90
c = 116.852γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.2165.5122974

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1MI52.2165.5121787118697.390.217560.214230.210650.27836RANDOM29.463
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]
-1.26-0.521.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.122
r_dihedral_angle_4_deg18.119
r_dihedral_angle_3_deg17.998
r_dihedral_angle_1_deg6.066
r_scangle_it5.036
r_scbond_it3.714
r_mcangle_it2.405
r_mcbond_it1.44
r_angle_refined_deg1.25
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.122
r_dihedral_angle_4_deg18.119
r_dihedral_angle_3_deg17.998
r_dihedral_angle_1_deg6.066
r_scangle_it5.036
r_scbond_it3.714
r_mcangle_it2.405
r_mcbond_it1.44
r_angle_refined_deg1.25
r_nbtor_refined0.299
r_symmetry_vdw_refined0.224
r_nbd_refined0.199
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.145
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms3527
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement