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Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8, Antigen-presenting glycoprotein CD1d, and Beta-2-microglobulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PO6 PDB entry 2PO6, 4WW1 experimental model PDB 4WW1 PDB entry 2PO6, 4WW1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 9-10% PEG 6K
0.1M MES 6.0
4% Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.78 55.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.99 α = 90 b = 46.3 β = 122.28 c = 124.65 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 QUANTUM 315r 2013-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.7108 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 2.48 44.8 99.5 8.2 4.6 36324 51.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.58 97.3 1.6 4.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2PO6, 4WW1 2.48 44.8 36324 1815 99.26 0.1981 0.1957 0.2439 0.2753 RANDOM 56.4
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] 0.789 -0.2764 -1.6818 0.8929
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.02 t_other_torsion 2.79 t_angle_deg 1.03 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.02 t_other_torsion 2.79 t_angle_deg 1.03 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6284 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 86
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing