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Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IWG 6IWG, 2NW2 experimental model PDB 2NW2 6IWG, 2NW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5 and 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.62 52.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.937 α = 90 b = 95.071 β = 90.894 c = 123.352 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX225HE 2019-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 2.8 50 99.7 0.098 12.02 3.8 48069 51.1104457323
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 2.8 2.95 0.492
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6IWG, 2NW2 2.80003270022 41.9633912528 1.36364223881 47838 2393 99.7643427666 0.188415640165 0.185170315463 0.1934 0.249628129727 0.2501 45.6531146715
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.5349846553 f_angle_d 1.45943770072 f_chiral_restr 0.0738702016494 f_bond_d 0.0121505773542 f_plane_restr 0.00774887625382
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13174 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling MOLREP phasing