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The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001034732-1 (trans-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 2.85 56.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.511 α = 90 b = 89.511 β = 90 c = 131.519 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 2.53 74 99.7 0.041 0.019 1 21 5.3 9220 65.13
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 2.53 2.63 0.551 0.277 0.781 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 2.53 45.6 1.33 9209 450 99.38 0.2194 0.217 0.2178 0.2687 0.27 83.76
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 11.143 f_angle_d 0.4913 f_chiral_restr 0.0373 f_plane_restr 0.0029 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1435 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 84
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing