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The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001034732-2 (cis-form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 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 3.01 59.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.98 α = 90 b = 90.98 β = 90 c = 134.738 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 2021-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.89 75.4 99.2 0.07 0.032 0.999 18.6 5.8 6568 83.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 3.07 99.3 0.93 0.418 0.789 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 5vpt 2.89 38.95 1.34 6496 307 97.55 0.2511 0.2495 0.2497 0.2831 0.2825 95.38
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 20.1093 f_angle_d 0.6646 f_chiral_restr 0.0447 f_plane_restr 0.0037 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1411 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 84
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing