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Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EYS PDB entry 2EYS followed by PDB entry 1ZT4 (without alpha-Galcer) experimental model PDB 1ZT4 PDB entry 2EYS followed by PDB entry 1ZT4 (without alpha-Galcer)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 13% PEG 10K, 0.1M bis-tris propane, 0.2M tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.62 66.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.012 α = 90 b = 155.636 β = 94.78 c = 85.981 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 CCD ADSC QUANTUM 210 2007-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
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 30 95.3 0.138 6.4 3.1 42581
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 3.31 74.7 0.486 1.8 3310
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 PDB entry 2EYS followed by
PDB entry 1ZT4 (without alpha-Galcer) 3.2 29.18 42133 2135 95.58 0.229 0.226 0.2174 0.293 0.2783 RANDOM 57.718
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] 0.18 -0.14 -0.01 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.069 r_dihedral_angle_3_deg 19.437 r_dihedral_angle_4_deg 17.605 r_dihedral_angle_1_deg 5.984 r_angle_refined_deg 1.151 r_scangle_it 0.833 r_scbond_it 0.476 r_mcangle_it 0.396 r_nbtor_refined 0.303 r_mcbond_it 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.069 r_dihedral_angle_3_deg 19.437 r_dihedral_angle_4_deg 17.605 r_dihedral_angle_1_deg 5.984 r_angle_refined_deg 1.151 r_scangle_it 0.833 r_scbond_it 0.476 r_mcangle_it 0.396 r_nbtor_refined 0.303 r_mcbond_it 0.216 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.182 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.085 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13083 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 215
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOSFLM data reduction MOLREP phasing