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Structure of mouse Va14Vb8.2NKT TCR-mouse CD1d-a-C-Galactosylceramide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HE6 PDB entry 3HE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 15-17% PEG 10K, 0.1M ammonium acetat, 0.1M BisTris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.12 60.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.171 α = 90 b = 86.368 β = 90 c = 236.403 γ = 90
Symmetry Space Group P 21 21 21
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 QUANTUM 315r 2010-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95453 Australian Synchrotron MX2
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 3.2 50 100 0.272 7.2 8.1 20725 20725 56.5
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 3.2 3.37 100 1.08 2.2 8.4 2959
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3HE6 3.2 48.77 19755 19666 1056 99.55 0.2286 0.2286 0.22537 0.2222 0.2887 0.2813 81.224
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] 0.63 7.32 -7.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.737 r_dihedral_angle_4_deg 19.366 r_dihedral_angle_3_deg 17.564 r_dihedral_angle_1_deg 5.437 r_angle_refined_deg 1.005 r_scangle_it 0.761 r_scbond_it 0.442 r_mcangle_it 0.344 r_mcbond_it 0.177 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.737 r_dihedral_angle_4_deg 19.366 r_dihedral_angle_3_deg 17.564 r_dihedral_angle_1_deg 5.437 r_angle_refined_deg 1.005 r_scangle_it 0.761 r_scbond_it 0.442 r_mcangle_it 0.344 r_mcbond_it 0.177 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6471 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 116
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling