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Influenza A/California/04/2009 (pH1N1) endonuclease with bound inhibitor, baloxavir acid (BXA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AWK PDB:4AWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml).
Mother liquor was 0.3 M (NH4)2SO4, 0.1 M ADA pH 6.5, 28% (w/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.3 46.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.18 α = 90 b = 75.69 β = 90 c = 121.59 γ = 90
Symmetry Space Group P 21 21 2
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 R 4M 2017-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.29 90.401 99.9 0.083 0.999 14.8 6.9 59550
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.34 100 0.908 0.77 2.2 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB:4AWK 2.291 90.401 0.31 56754 2796 99.81 0.1953 0.1934 0.2067 0.2306 0.2442
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 15.606 f_angle_d 0.847 f_chiral_restr 0.046 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8796 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 216
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing