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Structure and binding kinetics of three different human CD1d-alpha- Galactosylceramide-specific T cell receptors (TCR 5E)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGA PDB ENTRY 1OGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 200 MM MAGNESIUM SULPHATE, 20 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.27 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.451 α = 90 b = 64.451 β = 90 c = 184.977 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2003-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.25 30 98.8 0.07 31 12.4 21795 0.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.3 89.5 0.24 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OGA 2.25 30 20555 1098 98.7 0.192 0.188 0.2053 0.269 0.2851 RANDOM 30.59
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 -0.08 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.751 r_dihedral_angle_3_deg 18.344 r_dihedral_angle_4_deg 15.563 r_dihedral_angle_1_deg 6.997 r_scangle_it 5.858 r_mcangle_it 4.963 r_scbond_it 4.566 r_mcbond_it 3.942 r_angle_refined_deg 1.418 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.751 r_dihedral_angle_3_deg 18.344 r_dihedral_angle_4_deg 15.563 r_dihedral_angle_1_deg 6.997 r_scangle_it 5.858 r_mcangle_it 4.963 r_scbond_it 4.566 r_mcbond_it 3.942 r_angle_refined_deg 1.418 r_nbtor_refined 0.298 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 3436 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing