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human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGA 1OGA, 3QDJ experimental model PDB 3QDJ 1OGA, 3QDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG3350 8 %, K Thiocyanate 0.1 M, Bis-Tris propane pH 6.5 0.1 M, protein concentration 3.5 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.71 54.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 222.077 α = 90 b = 49.284 β = 97.61 c = 96.133 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 110 CCD ADSC QUANTUM 315r Si with Pt coating 2015-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979742 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 3.2 16 98.5 0.142 0.99 4.79 3.66 17189 62.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.29 98.8 0.561 0.86 1.26 3.7
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 1OGA, 3QDJ 3.2 16 14934 796 90.17 0.21735 0.21293 0.216 0.29874 0.3017 RANDOM 72.846
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] -8.71 -3.9 6.96 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.244 r_dihedral_angle_3_deg 20.405 r_dihedral_angle_4_deg 14.406 r_long_range_B_refined 8.923 r_long_range_B_other 8.923 r_dihedral_angle_1_deg 8.084 r_mcangle_other 5.812 r_mcangle_it 5.811 r_scangle_other 4.675 r_mcbond_it 3.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.244 r_dihedral_angle_3_deg 20.405 r_dihedral_angle_4_deg 14.406 r_long_range_B_refined 8.923 r_long_range_B_other 8.923 r_dihedral_angle_1_deg 8.084 r_mcangle_other 5.812 r_mcangle_it 5.811 r_scangle_other 4.675 r_mcbond_it 3.355 r_mcbond_other 3.355 r_scbond_it 2.63 r_scbond_other 2.628 r_angle_refined_deg 1.352 r_angle_other_deg 0.937 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6606 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing