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Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro globulin, presenting DFEREGYSL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 PACT screen, condition D02: 0.1M MMT Buffer, pH 5.0, 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 2.25 45.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.388 α = 81.24 b = 60.288 β = 67.59 c = 65.645 γ = 67.94
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 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) 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 2.14 55.87 96.9 0.128 0.172 0.115 0.979 3.4 1.9 41686
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 2.14 2.2 96 0.669 0.91 0.614 0.522 1.9 3024
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 3QQ3 2.14 55.87 39657 2021 96.88 0.2226 0.2195 0.2233 0.283 0.2879 RANDOM 28.043
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] -1.74 -0.23 -0.32 0.01 0.29 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.258 r_dihedral_angle_4_deg 21.301 r_dihedral_angle_3_deg 18.145 r_dihedral_angle_1_deg 7.289 r_angle_refined_deg 1.931 r_angle_other_deg 1.115 r_chiral_restr 0.125 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.258 r_dihedral_angle_4_deg 21.301 r_dihedral_angle_3_deg 18.145 r_dihedral_angle_1_deg 7.289 r_angle_refined_deg 1.931 r_angle_other_deg 1.115 r_chiral_restr 0.125 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6294 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 28
Software Software Software Name Purpose Aimless data scaling DIALS data reduction REFMAC refinement PDB_EXTRACT data extraction PHASER phasing xia2 data reduction