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Structure of the Mid-Cap-627 linker domains of the H5N1 influenza A PB2 subunit in complex with onradivir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EUV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.1 M HEPES, pH 7.0, 30% v/v Jeffamine ED-2001, pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.91 35.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.559 α = 90 b = 59.377 β = 107.566 c = 53.953 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2024-09-18 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 1.45 59.38 97.4 0.111 10.6 6.2 42193 9.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 0.469
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.45 51.44 1.36 42171 2171 97.34 0.1237 0.121 0.1347 0.173 0.1724 15.35
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.4249 f_angle_d 0.9659 f_chiral_restr 0.0739 f_plane_restr 0.0117 f_bond_d 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2243 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing