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'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro globulin, presenting EFEDLTFLA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5QQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 JBS screen, condition A07: 30% MPD, 100 mM Na Citrate, pH 5.6, 200 mM Ammonium Acetate
Crystal Properties Matthews coefficient Solvent content 2.27 45.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.301 α = 81.48 b = 59.696 β = 67.62 c = 66.443 γ = 68.6
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 X 6M 2016-07-07 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) 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 1.57 61.44 96 0.06 5.7 1.9 105240 23
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 1.57 1.61 93.3 0.665 1.9
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 5QQ3 1.57 61.44 99669 5113 95.61 0.21989 0.21772 0.2242 0.26232 0.2671 RANDOM 26.823
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] -0.91 0.07 0.14 0.17 0.44 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.501 r_dihedral_angle_4_deg 18.82 r_dihedral_angle_3_deg 16.436 r_dihedral_angle_1_deg 6.679 r_long_range_B_refined 6.043 r_long_range_B_other 5.885 r_scangle_other 2.267 r_angle_refined_deg 1.818 r_mcangle_it 1.54 r_mcangle_other 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.501 r_dihedral_angle_4_deg 18.82 r_dihedral_angle_3_deg 16.436 r_dihedral_angle_1_deg 6.679 r_long_range_B_refined 6.043 r_long_range_B_other 5.885 r_scangle_other 2.267 r_angle_refined_deg 1.818 r_mcangle_it 1.54 r_mcangle_other 1.54 r_scbond_it 1.474 r_scbond_other 1.47 r_angle_other_deg 1.058 r_mcbond_it 0.969 r_mcbond_other 0.969 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 6290 Nucleic Acid Atoms Solvent Atoms 795 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction PDB_EXTRACT data extraction DIALS data reduction PHASER phasing