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Crystal structure of 9-mer peptide from H5N1 avian influenza virus in complex with B4 DUCK MHC I (UAA*76)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 Salt: none
Buffer: 0.04 M Citric acid, 0.06 M BIS-TRIS propane / pH 6.4
Polymer: 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.094 α = 90 b = 82.094 β = 90 c = 111.37 γ = 120
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 2024-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979230 SSRF BL19U1
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 2.5 44 99.2 0.069 22.9 9.1 14802
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 2.5 2.6 0.166
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.501 43.839 14666 734 99.262 0.18 0.1764 0.1828 0.2469 0.2514 29.37
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] 0.003 0.001 0.003 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.853 r_dihedral_angle_6_deg 16.759 r_dihedral_angle_2_deg 7.858 r_lrange_it 7.197 r_lrange_other 7.195 r_dihedral_angle_1_deg 6.629 r_scangle_it 5.298 r_scangle_other 5.297 r_mcangle_it 4.023 r_mcangle_other 4.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.853 r_dihedral_angle_6_deg 16.759 r_dihedral_angle_2_deg 7.858 r_lrange_it 7.197 r_lrange_other 7.195 r_dihedral_angle_1_deg 6.629 r_scangle_it 5.298 r_scangle_other 5.297 r_mcangle_it 4.023 r_mcangle_other 4.022 r_scbond_it 3.394 r_scbond_other 3.393 r_mcbond_it 2.588 r_mcbond_other 2.584 r_angle_refined_deg 1.401 r_angle_other_deg 0.477 r_symmetry_xyhbond_nbd_refined 0.261 r_xyhbond_nbd_refined 0.232 r_nbd_refined 0.211 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.186 r_nbd_other 0.169 r_symmetry_nbd_refined 0.098 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3095 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing