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Structures of HLA-B8E76C loaded with long peptides reveal novel features at the N-terminus of the groove
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P2S 6P2S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 298 0.2 M ammonium acetate, 18% PEG 4000, 0.1 M sodium citrate,
Crystal Properties Matthews coefficient Solvent content 2.54 51.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.577 α = 90 b = 81.273 β = 90 c = 110.498 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 CCD MARMOSAIC 300 mm CCD 2020-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G
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 1.37 65.47 99.5 0.068 29.1 4.2 95762
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 1.37 1.42 97 0.48 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6P2S 1.37 27 90865 4895 99.42 0.1682 0.166 0.1683 0.21 0.2151 RANDOM 18.537
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] -1.17 -1.12 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.261 r_dihedral_angle_4_deg 18.968 r_sphericity_free 18.69 r_sphericity_bonded 16.655 r_dihedral_angle_3_deg 13.631 r_dihedral_angle_1_deg 6.663 r_rigid_bond_restr 4.515 r_angle_refined_deg 2.115 r_angle_other_deg 1.522 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.261 r_dihedral_angle_4_deg 18.968 r_sphericity_free 18.69 r_sphericity_bonded 16.655 r_dihedral_angle_3_deg 13.631 r_dihedral_angle_1_deg 6.663 r_rigid_bond_restr 4.515 r_angle_refined_deg 2.115 r_angle_other_deg 1.522 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3148 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling