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HLA A*2402-NF9_6F pMHC complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Glycerol 15% v/v
Polyethylene Glycol 4,000, 20% w/v
MES, 0.1 M, pH7
Crystal Properties Matthews coefficient Solvent content 2.41 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 344.797 α = 90 b = 84.336 β = 102.14 c = 91.453 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 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 2.6 87 100 0.179 0.193 0.072 0.995 7.7 7.1 79258
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 2.6 2.65 99.5 1.738 1.887 0.73 0.465 6.6
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 2.6 87 75257 3966 99.91 0.2262 0.22417 0.2252 0.26431 0.2648 RANDOM 63.237
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] -1.4 -2.38 -0.05 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.777 r_dihedral_angle_3_deg 17.385 r_dihedral_angle_4_deg 16.277 r_dihedral_angle_1_deg 6.774 r_long_range_B_refined 4.148 r_long_range_B_other 4.146 r_scangle_other 2.424 r_mcangle_it 2.204 r_mcangle_other 2.204 r_scbond_it 1.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.777 r_dihedral_angle_3_deg 17.385 r_dihedral_angle_4_deg 16.277 r_dihedral_angle_1_deg 6.774 r_long_range_B_refined 4.148 r_long_range_B_other 4.146 r_scangle_other 2.424 r_mcangle_it 2.204 r_mcangle_other 2.204 r_scbond_it 1.462 r_scbond_other 1.462 r_angle_refined_deg 1.372 r_mcbond_it 1.307 r_mcbond_other 1.307 r_angle_other_deg 1.156 r_chiral_restr 0.057 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 18990 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing