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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 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 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.263 α = 90 b = 145.255 β = 119.771 c = 82.838 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER2 S 9M 2024-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979183 SSRF BL02U1
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 1.61 35.952 100 0.134 8 6.5 108727
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 1.61 1.65 1.36
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 1.61 35.952 108695 5352 99.957 0.192 0.1905 0.1995 0.225 0.2314 18.772
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] -0.001 -0.002 0.002 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.647 r_dihedral_angle_3_deg 14.193 r_lrange_it 6.396 r_dihedral_angle_1_deg 6.389 r_lrange_other 6.348 r_dihedral_angle_2_deg 6.34 r_scangle_it 5.314 r_scangle_other 5.313 r_scbond_it 3.396 r_scbond_other 3.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.647 r_dihedral_angle_3_deg 14.193 r_lrange_it 6.396 r_dihedral_angle_1_deg 6.389 r_lrange_other 6.348 r_dihedral_angle_2_deg 6.34 r_scangle_it 5.314 r_scangle_other 5.313 r_scbond_it 3.396 r_scbond_other 3.396 r_mcangle_it 2.757 r_mcangle_other 2.757 r_mcbond_it 1.894 r_mcbond_other 1.894 r_angle_refined_deg 1.514 r_angle_other_deg 0.528 r_nbd_refined 0.208 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.186 r_nbd_other 0.182 r_xyhbond_nbd_refined 0.18 r_symmetry_nbd_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.131 r_ncsr_local_group_2 0.105 r_ncsr_local_group_1 0.093 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6184 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing