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P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 di-Sodium malonate, 0.1M
HEPES pH7, 0.1M
Poly(acrylic acid sodium salt) 2,100, 30% w/v
Crystal Properties Matthews coefficient Solvent content 4.75 74.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.41 α = 90 b = 200.41 β = 90 c = 156.336 γ = 120
Symmetry Space Group P 31 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 100 PIXEL DECTRIS EIGER2 XE 16M 2022-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.1 60.63 100 0.293 0.3 0.065 0.997 8.8 21 65958
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.18 100 3.851 3.941 0.833 0.407 22
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.1 60.56 62481 3393 99.9 0.19158 0.18948 0.1935 0.23066 0.2332 RANDOM 112.331
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] -4.78 -2.39 -4.78 15.52
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 30.147 r_long_range_B_other 30.147 r_mcangle_it 22.65 r_mcangle_other 22.649 r_scangle_other 20.406 r_dihedral_angle_3_deg 16.679 r_mcbond_it 14.468 r_mcbond_other 14.468 r_scbond_it 12.712 r_scbond_other 12.71
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 30.147 r_long_range_B_other 30.147 r_mcangle_it 22.65 r_mcangle_other 22.649 r_scangle_other 20.406 r_dihedral_angle_3_deg 16.679 r_mcbond_it 14.468 r_mcbond_other 14.468 r_scbond_it 12.712 r_scbond_other 12.71 r_dihedral_angle_1_deg 6.759 r_dihedral_angle_2_deg 6.046 r_rigid_bond_restr 3.199 r_angle_refined_deg 1.504 r_angle_other_deg 0.525 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13408 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction