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Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta8.2 NKT TCR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FIK 2FIK, 2Q86 experimental model PDB 2Q86 2FIK, 2Q86
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 17% polyethylene glycol 10K, 0.1M ammonium acetate, 0.1M BisTris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.02 59.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.113 α = 90 b = 81.506 β = 90 c = 233.451 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 210 2008-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95667 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.9 50 100 0.166 0.166 11.1 5.6 26743 26743 1 1 69.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 100 0.714 0.714 2.1 6 3814
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 2FIK, 2Q86 2.9 50 1 1 25363 25363 1344 99.85 0.23716 0.23389 0.2654 0.29846 0.3103 RANDOM 48.885
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] 3.08 1.53 -4.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.329 r_dihedral_angle_3_deg 17.231 r_dihedral_angle_4_deg 16.605 r_dihedral_angle_1_deg 5.685 r_angle_refined_deg 1.076 r_scangle_it 0.954 r_scbond_it 0.558 r_mcangle_it 0.407 r_nbtor_refined 0.3 r_mcbond_it 0.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.329 r_dihedral_angle_3_deg 17.231 r_dihedral_angle_4_deg 16.605 r_dihedral_angle_1_deg 5.685 r_angle_refined_deg 1.076 r_scangle_it 0.954 r_scbond_it 0.558 r_mcangle_it 0.407 r_nbtor_refined 0.3 r_mcbond_it 0.226 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6559 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 116
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling