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Crystal structure of mouse CD1d-alpha-phosphotidylinositol with mouse Valpha14-Vbeta6 2A3-D NKT TCR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HE7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 296 PEG 6000, Sodium Citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.44 64.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.697 α = 90 b = 95.697 β = 90 c = 289.71 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.47 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 41 15.3 13.3 69852
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 3HE7 2.3 39.31 60849 3082 99.93 0.2484 0.247 0.2491 0.2749 0.2748 RANDOM 54.3635
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] -0.43 -0.43 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.631 r_dihedral_angle_4_deg 17.415 r_dihedral_angle_3_deg 14.146 r_dihedral_angle_1_deg 5.117 r_angle_refined_deg 0.976 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6558 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing