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HLA A*2402-NF9_5R pMHC complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Glycerol 15% v/v
Polyethylene glycol 4000, 20% w/v
Sodium Cacodylate, 0.1 M, pH 6
Crystal Properties Matthews coefficient Solvent content 2.31 46.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.281 α = 90 b = 77.018 β = 110.58 c = 111.82 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 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 2.3 54.8 99.6 0.156 0.168 0.063 0.996 8 7 73135
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 2.3 2.35 96.3 1.191 1.289 0.489 0.677 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 54.8 69442 3589 99.7 0.21927 0.21686 0.26524 0.24 RANDOM 39.207
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] 2.19 -0.78 -0.96 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.421 r_dihedral_angle_4_deg 18.348 r_dihedral_angle_3_deg 18.303 r_dihedral_angle_1_deg 8.388 r_long_range_B_refined 3.787 r_long_range_B_other 3.774 r_scangle_other 1.958 r_mcangle_it 1.583 r_mcangle_other 1.583 r_angle_refined_deg 1.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.421 r_dihedral_angle_4_deg 18.348 r_dihedral_angle_3_deg 18.303 r_dihedral_angle_1_deg 8.388 r_long_range_B_refined 3.787 r_long_range_B_other 3.774 r_scangle_other 1.958 r_mcangle_it 1.583 r_mcangle_other 1.583 r_angle_refined_deg 1.447 r_angle_other_deg 1.201 r_scbond_it 1.18 r_scbond_other 1.18 r_mcbond_it 0.946 r_mcbond_other 0.946 r_chiral_restr 0.066 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 12676 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing DIALS data reduction