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Crystal Structure of 9C2 TCR bound to CD1d
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LFH PDB ENTRIES 4LFH AND 2PO6 experimental model PDB 2PO6 PDB ENTRIES 4LFH AND 2PO6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 12% PEG8000, 0.1 M Tris-HCl, pH 7.0, 0.2 M magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.45 64.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.62 α = 90 b = 152.69 β = 90 c = 135.2 γ = 90
Symmetry Space Group C 2 2 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 2013-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.869 99.692 99.1 0.135 10.9 31239 31239 92.67
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 2.869 3.02 94 0.518 2 10.5
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 4LFH AND 2PO6 2.87 47.47 31198 1579 99.14 0.2077 0.2059 0.2228 0.2431 0.2621 RANDOM 118.16
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] -7.7615 1.312 6.4495
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.48 t_omega_torsion 2.47 t_angle_deg 1.06 t_bond_d 0.009 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_other_torsion 3.48 t_omega_torsion 2.47 t_angle_deg 1.06 t_bond_d 0.009 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 6460 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 180
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