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Engineered Human HLA_A2 MHC Class I molecule in complex with NV9 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MRE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 5 mM cobalt chloride, 5 mM cadmium chloride, 5 mM magnesium chloride, 5 mM nickel chloride,
0.1 M HEPES pH 7.5, 12 % PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.97 58.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.158 α = 90 b = 80.575 β = 90 c = 109.693 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 100 PIXEL DECTRIS PILATUS3 S 6M 2017-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.5 65 99.9 0.055 7.3 5.4 81571
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53
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 3MRE 1.5 64.94 81571 4265 99.85 0.17552 0.17428 0.1754 0.19955 0.1998 RANDOM 23.012
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] -0.73 0.65 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.961 r_dihedral_angle_4_deg 20.309 r_dihedral_angle_3_deg 13.235 r_dihedral_angle_1_deg 11.111 r_long_range_B_refined 8.581 r_long_range_B_other 8.363 r_scangle_other 6.574 r_scbond_it 4.549 r_scbond_other 4.541 r_mcangle_it 3.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.961 r_dihedral_angle_4_deg 20.309 r_dihedral_angle_3_deg 13.235 r_dihedral_angle_1_deg 11.111 r_long_range_B_refined 8.581 r_long_range_B_other 8.363 r_scangle_other 6.574 r_scbond_it 4.549 r_scbond_other 4.541 r_mcangle_it 3.919 r_mcangle_other 3.918 r_mcbond_other 2.875 r_mcbond_it 2.874 r_angle_refined_deg 1.508 r_angle_other_deg 0.782 r_chiral_restr 0.123 r_gen_planes_refined 0.015 r_bond_refined_d 0.013 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 3142 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing