3QUY

Structure of the mouse CD1d-BnNH-GSL-1'-iNKT TCR complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QY7PDB entries 2QY7, 3HE6
experimental modelPDB 3HE6PDB entries 2QY7, 3HE6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529517% polyethylene glycol 4000, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.0259.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.765α = 90
b = 192.005β = 90
c = 150.922γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.976SSRLBL7-1

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
12.255099.50.0919.53.65355753289
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)
12.252.3199.80.5722.13.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB entries 2QY7, 3HE62.2535.3553289111299.650.190370.189520.23073RANDOM40.574
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]
-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.464
r_dihedral_angle_4_deg14.274
r_dihedral_angle_3_deg13.553
r_dihedral_angle_1_deg6.376
r_scangle_it2.953
r_scbond_it1.853
r_angle_refined_deg1.349
r_mcangle_it1.067
r_mcbond_it0.56
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.464
r_dihedral_angle_4_deg14.274
r_dihedral_angle_3_deg13.553
r_dihedral_angle_1_deg6.376
r_scangle_it2.953
r_scbond_it1.853
r_angle_refined_deg1.349
r_mcangle_it1.067
r_mcbond_it0.56
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms6262
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms140

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling