3ARB

Ternary crystal structure of the NKT TCR-CD1d-alpha-galactosylceramide analogue-OCH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HE6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629522% PEG 400, 0.1M Ammonium acetate, 0.1M Bis Tris, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.1561.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.037α = 90
b = 87.309β = 90
c = 235.654γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95453Australian SynchrotronMX2

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
12.75095.90.0919.33.6341413274168
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)
12.72.8597.40.582.13.64882

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT3HE62.748.843272631106163595.050.216170.216170.213990.25673RANDOM56.06
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]
-0.514.77-4.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.448
r_dihedral_angle_4_deg14.472
r_dihedral_angle_3_deg13.813
r_dihedral_angle_1_deg4.766
r_angle_refined_deg0.943
r_scangle_it0.65
r_scbond_it0.381
r_mcangle_it0.296
r_mcbond_it0.153
r_chiral_restr0.061
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.448
r_dihedral_angle_4_deg14.472
r_dihedral_angle_3_deg13.813
r_dihedral_angle_1_deg4.766
r_angle_refined_deg0.943
r_scangle_it0.65
r_scbond_it0.381
r_mcangle_it0.296
r_mcbond_it0.153
r_chiral_restr0.061
r_bond_refined_d0.005
r_gen_planes_refined0.003
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 Atoms6470
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms163

Software

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