☰ Navigation Tabs
Crystal structure of Paraoxonase from Bacillus sp. strain S3wahi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M MES monohydrate pH 6.5
1.6 M Magensium sulfate heptahydrate
Crystal Properties Matthews coefficient Solvent content 2.86 56.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.823 α = 90 b = 77.823 β = 90 c = 135.266 γ = 90
Symmetry Space Group P 41 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 293.15 PIXEL DECTRIS EIGER X 16M 2024-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.494 39.01 100 0.043 0.044 0.012 29.4 13.3 67871 2 26.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.494 1.52 99.25 2.083 2.164 0.579 13.47
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold 1.494 39.01 67871 99.901 0.185 0.183 0.1854 0.195 0.1844 34.89
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] 0.739 0.739 -1.477
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 42.963 r_lrange_other 42.943 r_scangle_it 18.591 r_scangle_other 18.586 r_mcangle_it 16.784 r_mcangle_other 16.784 r_dihedral_angle_3_deg 16.261 r_dihedral_angle_6_deg 14.867 r_dihedral_angle_2_deg 14.491 r_scbond_other 14.28
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 42.963 r_lrange_other 42.943 r_scangle_it 18.591 r_scangle_other 18.586 r_mcangle_it 16.784 r_mcangle_other 16.784 r_dihedral_angle_3_deg 16.261 r_dihedral_angle_6_deg 14.867 r_dihedral_angle_2_deg 14.491 r_scbond_other 14.28 r_scbond_it 14.276 r_mcbond_it 12.159 r_mcbond_other 12.148 r_dihedral_angle_1_deg 7.029 r_rigid_bond_restr 5.508 r_angle_refined_deg 1.959 r_symmetry_nbd_refined 1.119 r_xyhbond_nbd_other 0.999 r_symmetry_xyhbond_nbd_refined 0.805 r_angle_other_deg 0.755 r_nbd_other 0.728 r_nbd_refined 0.234 r_symmetry_nbd_other 0.23 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2365 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building MOLREP phasing Aimless data scaling