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Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta7 NKT TCR
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 5.5 298 17% polyethylene glycol 10K, 0.1M ammonium acetate, 0.1M Bis Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3 58.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.229 α = 90 b = 81.913 β = 90 c = 243.253 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 2008-09-14 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 2.8 50 99.7 0.132 0.132 13.7 7 29526 29526 1 1 61.2
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 2.8 2.95 99.1 0.707 0.707 2.2 5.8 4192
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 3HE6 2.8 50 1 1 28041 28041 1480 99.65 0.22614 0.22368 0.245 0.27117 0.2848 RANDOM 44.162
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] 0.95 0.74 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.532 r_dihedral_angle_3_deg 16.983 r_dihedral_angle_4_deg 16.185 r_dihedral_angle_1_deg 5.476 r_angle_refined_deg 1.029 r_scangle_it 0.914 r_scbond_it 0.545 r_mcangle_it 0.403 r_nbtor_refined 0.299 r_mcbond_it 0.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.532 r_dihedral_angle_3_deg 16.983 r_dihedral_angle_4_deg 16.185 r_dihedral_angle_1_deg 5.476 r_angle_refined_deg 1.029 r_scangle_it 0.914 r_scbond_it 0.545 r_mcangle_it 0.403 r_nbtor_refined 0.299 r_mcbond_it 0.229 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.145 r_symmetry_hbond_refined 0.12 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6528 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 116
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling