☰ Navigation Tabs
The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988514
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 2.89 57.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.596 α = 90 b = 89.596 β = 90 c = 133.159 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 2021-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 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 2.37 74.34 99.3 0.044 0.02 1 19.8 5.8 11241 58.01
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 2.37 2.46 99.8 0.957 0.431 0.817 1.9
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 2.37 38.37 1.34 11234 521 98.7 0.2221 0.2203 0.2205 0.2585 0.2611 77.27
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 16.4403 f_angle_d 0.5108 f_chiral_restr 0.0389 f_plane_restr 0.0029 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1434 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 96
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing