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Porcine (Sus scrofa) Major Histocompatibility Complex, class I, 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 A09: 0.2 M LiCl, 0.1 M Sodium Acetate, pH 5.0, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.66 53.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.616 α = 104.36 b = 46.34 β = 101.21 c = 66.735 γ = 102.2
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 2017-01-18 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) 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 1.1 39.28 92.3 0.086 0.998 6 1.9 170825
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.13 83.1 0.179 0.596 1.1 1.7
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 1.1 39.27 161372 8412 91.63 0.18999 0.18903 0.1986 0.20852 0.218 RANDOM 17.308
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] 0.48 -0.25 -0.14 0.06 0.02 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.145 r_dihedral_angle_4_deg 16.823 r_dihedral_angle_3_deg 13.646 r_long_range_B_refined 6.823 r_long_range_B_other 6.576 r_dihedral_angle_1_deg 6.211 r_angle_refined_deg 2.127 r_scangle_other 1.595 r_mcangle_it 1.076 r_mcangle_other 1.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.145 r_dihedral_angle_4_deg 16.823 r_dihedral_angle_3_deg 13.646 r_long_range_B_refined 6.823 r_long_range_B_other 6.576 r_dihedral_angle_1_deg 6.211 r_angle_refined_deg 2.127 r_scangle_other 1.595 r_mcangle_it 1.076 r_mcangle_other 1.075 r_angle_other_deg 1.064 r_scbond_it 1.045 r_scbond_other 1.04 r_mcbond_it 0.645 r_mcbond_other 0.645 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.007 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 3117 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data reduction Aimless data scaling PHASER phasing