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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 pH 7.5
0.09M NPS
0.1 M Buffer system 2
37.5% v/v MPD_P1K_P3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.457 α = 90 b = 82.457 β = 90 c = 111.883 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 0.97923 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 2.35 44.25 98.4 1.723 10.6 14.5 18023
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 2.35 2.39 0.009
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 2.352 44.038 17587 880 97.923 0.191 0.1874 0.1955 0.2556 0.2612 24.658
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] 0.005 0.002 0.005 -0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.107 r_dihedral_angle_6_deg 16.263 r_dihedral_angle_2_deg 10.737 r_lrange_other 6.756 r_lrange_it 6.751 r_dihedral_angle_1_deg 6.688 r_scangle_it 5.336 r_scangle_other 5.335 r_mcangle_it 3.512 r_mcangle_other 3.512
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.107 r_dihedral_angle_6_deg 16.263 r_dihedral_angle_2_deg 10.737 r_lrange_other 6.756 r_lrange_it 6.751 r_dihedral_angle_1_deg 6.688 r_scangle_it 5.336 r_scangle_other 5.335 r_mcangle_it 3.512 r_mcangle_other 3.512 r_scbond_it 3.429 r_scbond_other 3.428 r_mcbond_it 2.254 r_mcbond_other 2.22 r_angle_refined_deg 1.44 r_angle_other_deg 0.501 r_xyhbond_nbd_refined 0.246 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.212 r_symmetry_nbd_other 0.198 r_nbd_other 0.193 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.087 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3099 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement