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MHC class I from a wild bird in complex with a nonameric peptide P2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GJX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM Hepes/MOPS, pH 7.0,
20 mM MgCl2, 40 mM CaCl2,
25 % (v/v) MPD, 25 % (w/v) PEG 1000, 25 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.202 α = 90 b = 48.78 β = 90 c = 202.135 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 EIGER X 16M 2019-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97940 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 67.38 99.9 0.999 12.1 13 22044
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 99.8 0.848 1.9 13.4
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 5GJX 2.15 50.58 20877 1102 99.92 0.18245 0.17984 0.1872 0.22937 0.2339 RANDOM 49.065
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] -2.95 1.87 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.961 r_dihedral_angle_4_deg 22.587 r_dihedral_angle_3_deg 19.37 r_dihedral_angle_1_deg 7.896 r_long_range_B_refined 6.477 r_long_range_B_other 6.477 r_scangle_other 3.843 r_mcangle_it 2.706 r_mcangle_other 2.706 r_scbond_other 2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.961 r_dihedral_angle_4_deg 22.587 r_dihedral_angle_3_deg 19.37 r_dihedral_angle_1_deg 7.896 r_long_range_B_refined 6.477 r_long_range_B_other 6.477 r_scangle_other 3.843 r_mcangle_it 2.706 r_mcangle_other 2.706 r_scbond_other 2.47 r_scbond_it 2.469 r_angle_refined_deg 1.837 r_mcbond_it 1.785 r_mcbond_other 1.784 r_angle_other_deg 1.389 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 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 3151 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 10
Software Software Software Name Purpose EDNA data collection XDS data reduction XDS data scaling PHASER phasing REFMAC refinement