2CDF

Structure and binding kinetics of three different human CD1d-alpha- Galactosylceramide-specific T cell receptors (TCR 5E)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OGAPDB ENTRY 1OGA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1200 MM MAGNESIUM SULPHATE, 20 % PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2744

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.451α = 90
b = 64.451β = 90
c = 184.977γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.253098.80.073112.4217950.5
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)
12.252.389.50.247.9

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 ENTRY 1OGA2.253020555109898.70.1920.1880.269RANDOM30.59
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]
-0.08-0.04-0.080.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.751
r_dihedral_angle_3_deg18.344
r_dihedral_angle_4_deg15.563
r_dihedral_angle_1_deg6.997
r_scangle_it5.858
r_mcangle_it4.963
r_scbond_it4.566
r_mcbond_it3.942
r_angle_refined_deg1.418
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.751
r_dihedral_angle_3_deg18.344
r_dihedral_angle_4_deg15.563
r_dihedral_angle_1_deg6.997
r_scangle_it5.858
r_mcangle_it4.963
r_scbond_it4.566
r_mcbond_it3.942
r_angle_refined_deg1.418
r_nbtor_refined0.298
r_nbd_refined0.206
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.187
r_xyhbond_nbd_refined0.185
r_chiral_restr0.1
r_bond_refined_d0.012
r_gen_planes_refined0.005
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3436
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing