3HE6

Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta8.2 NKT TCR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FIK2FIK, 2Q86
experimental modelPDB 2Q862FIK, 2Q86

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529817% polyethylene glycol 10K, 0.1M ammonium acetate, 0.1M BisTris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0259.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.113α = 90
b = 81.506β = 90
c = 233.451γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95667Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.9501000.1660.16611.15.626743267431169.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.93.061000.7140.7142.163814

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2FIK, 2Q862.950112536325363134499.850.237160.233890.29846RANDOM48.885
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]
3.081.53-4.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.329
r_dihedral_angle_3_deg17.231
r_dihedral_angle_4_deg16.605
r_dihedral_angle_1_deg5.685
r_angle_refined_deg1.076
r_scangle_it0.954
r_scbond_it0.558
r_mcangle_it0.407
r_nbtor_refined0.3
r_mcbond_it0.226
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.329
r_dihedral_angle_3_deg17.231
r_dihedral_angle_4_deg16.605
r_dihedral_angle_1_deg5.685
r_angle_refined_deg1.076
r_scangle_it0.954
r_scbond_it0.558
r_mcangle_it0.407
r_nbtor_refined0.3
r_mcbond_it0.226
r_nbd_refined0.19
r_symmetry_vdw_refined0.15
r_xyhbond_nbd_refined0.128
r_symmetry_hbond_refined0.128
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms6559
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms116

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling