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1E6 TCR in complex with HLA-A02 carrying RQFGPDFPTI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UTQ PDB entry 3UTQ for the MHC part and 4UTQ for the TCR part. experimental model PDB 4UTQ PDB entry 3UTQ for the MHC part and 4UTQ for the TCR part.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M HEPES, pH 7.5, 15% PEG 4000, 0.2M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.75 55.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.94 α = 96.98 b = 100.28 β = 98.05 c = 122.44 γ = 96.53
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97630 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.03 42.76 97.6 0.05 0.069 0.046 8 2 128366 128366
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.08 96.7 0.268 0.268 0.428 2.8 1.9 9447
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 3UTQ for the MHC part and 4UTQ for the TCR part. 2.03 42.76 121919 6446 97.55 0.194 0.1921 0.1978 0.2307 0.2344 RANDOM 52.559
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] 1.91 0.29 -0.77 0.95 0.6 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.023 r_dihedral_angle_4_deg 20.99 r_dihedral_angle_3_deg 19.315 r_dihedral_angle_1_deg 7.527 r_mcangle_it 2.306 r_angle_refined_deg 1.923 r_mcbond_other 1.504 r_mcbond_it 1.503 r_angle_other_deg 1.269 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.023 r_dihedral_angle_4_deg 20.99 r_dihedral_angle_3_deg 19.315 r_dihedral_angle_1_deg 7.527 r_mcangle_it 2.306 r_angle_refined_deg 1.923 r_mcbond_other 1.504 r_mcbond_it 1.503 r_angle_other_deg 1.269 r_chiral_restr 0.144 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13402 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 306
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction