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HLA class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane pH 7.5, 20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.96 α = 90 b = 121.29 β = 107.3 c = 68.96 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 PILATUS 6M 2016-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.95 60.64 99.6 0.1 0.144 0.995 8.3 3.7 64792 31.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.8 0.913 1.295 0.589 1.3 3.7
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 1.95 60.64 61597 3165 99.58 0.19539 0.19307 0.1995 0.2411 0.2441 RANDOM 38.763
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] 2.38 -0.14 0.4 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.97 r_dihedral_angle_4_deg 18.595 r_dihedral_angle_3_deg 15.267 r_dihedral_angle_1_deg 7.393 r_long_range_B_refined 7.083 r_long_range_B_other 7.048 r_scangle_other 4.603 r_mcangle_it 3.482 r_mcangle_other 3.482 r_scbond_it 3.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.97 r_dihedral_angle_4_deg 18.595 r_dihedral_angle_3_deg 15.267 r_dihedral_angle_1_deg 7.393 r_long_range_B_refined 7.083 r_long_range_B_other 7.048 r_scangle_other 4.603 r_mcangle_it 3.482 r_mcangle_other 3.482 r_scbond_it 3.074 r_scbond_other 3.026 r_mcbond_it 2.335 r_mcbond_other 2.324 r_angle_refined_deg 1.866 r_angle_other_deg 1.4 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 6351 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing