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I38T mutant of 2009 H1N1 PA Endonuclease in complex with RO-7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VP8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 291 0.1 M HEPES pH 7.8, 1 M Ammonium Sulfate, 10 mM MnCl2, 10 mM MgCl2, 0.5% PVP K15
Crystal Properties Matthews coefficient Solvent content 2.98 58.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.672 α = 90 b = 90.672 β = 90 c = 134.165 γ = 90
Symmetry Space Group I 4 2 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 CCD RAYONIX MX300-HS 2017-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 50 99.2 0.081 0.085 0.025 11 10.9 12668
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 92.9 0.774 0.834 0.3 0.809 6.7
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 THROUGHOUT 5VP8 2.303 38.816 1.35 12656 672 99.02 0.1951 0.1934 0.1983 0.2239 0.2283 76.5133
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 4.068 f_angle_d 1.067 f_chiral_restr 0.063 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1443 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction SERGUI data collection HKL data scaling