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Crystal Structure of XV19 TCR in complex with CD1d-sulfatide C24:1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AKR PDB ENTRIES 2AKR AND 4EI6 experimental model PDB 4EI6 PDB ENTRIES 2AKR AND 4EI6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 277 25% PEG3350, 0.1 M citrate/Bis-Tris-propane, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.95 58.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.739 α = 90 b = 140.711 β = 90 c = 160.773 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 315r 2012-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95453 Australian Synchrotron MX2
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 3.1 140 99 0.151 8.3 4.2 42432 42432 90.04
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 3.1 3.27 99.7 1.107 1.5 4.2 6151
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 ENTRIES 2AKR AND 4EI6 3.1 105.88 42390 2152 98.56 0.1988 0.1972 0.2134 0.2268 0.248 RANDOM 100.8742
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] -6.6184 19.9022 -13.2839
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.6 t_omega_torsion 2.29 t_angle_deg 1.04 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.6 t_omega_torsion 2.29 t_angle_deg 1.04 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 12928 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 275
Software Software Software Name Purpose SCALA data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction BUSTER refinement