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Ternary crystal structure of the mouse NKT TCR-CD1d-alpha-glucosylceramide(C20:2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 20% PEG 400, 0.1M Ammonium acetate, 0.1M Bis Tris, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.13 60.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.165 α = 90 b = 85.774 β = 90 c = 237.805 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 2009-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95367 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 50 94.5 0.218 9.4 10.4 24965 23592 61.1
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 3.16 95.9 1.083 2 10.5 3603
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 (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 3HE6 3 47.56 23958 22355 1198 93.31 0.23563 0.23222 0.228 0.29958 0.2932 RANDOM 67.513
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] 2.99 5.76 -8.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.744 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 16.948 r_dihedral_angle_1_deg 4.928 r_angle_refined_deg 0.992 r_scangle_it 0.626 r_scbond_it 0.379 r_mcangle_it 0.278 r_mcbond_it 0.142 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.744 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 16.948 r_dihedral_angle_1_deg 4.928 r_angle_refined_deg 0.992 r_scangle_it 0.626 r_scbond_it 0.379 r_mcangle_it 0.278 r_mcbond_it 0.142 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 6038 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 117
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling