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Structure and binding kinetics of three different human CD1d-alpha- Galactosylceramide specific T cell receptors - iNKT-TCR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MI5 PDB ENTRY 1MI5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.5 M NACL, 11 % PEG 8000, 50 MM HEPES PH7.0
Crystal Properties Matthews coefficient Solvent content 3.26 61.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 289.36 α = 90 b = 84.95 β = 103.3 c = 78.86 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 100 CCD ADSC CCD 2004-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 3.5 30 98.1 0.18 6.4 3.2 23622 0.5
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 3.5 3.62 90.9 0.88 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1MI5 3.5 30 0.5 23435 1193 98.9 0.283 0.283 0.2677 0.3504 0.3201 RANDOM
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] 2.291 -7.262 -17.073 14.782
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.19976 c_bond_d 0.005938 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.19976 c_bond_d 0.005938 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10330 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing