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Paraoxonase-1 in complex with terbium(III) and 2-hydroxyquinoline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.5 294 16% (w/v) PEG 3350, 0.1 M Bis-Tris Propane, pH 6.50, 0.2 M NaBr
Crystal Properties Matthews coefficient Solvent content 4.16 70.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.064 α = 90 b = 98.064 β = 90 c = 138.877 γ = 90
Symmetry Space Group P 43 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 100 PIXEL DECTRIS PILATUS 6M 2024-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.30 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.35 19.82 100 0.051 1 13.8 24.8 28693 43.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.4 1.073 0.41 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.35 19.82 1.33 28686 2605 99.97 0.192 0.1902 0.2285 0.2275 47.63
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 16.4952 f_angle_d 0.9025 f_chiral_restr 0.0583 f_bond_d 0.0078 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2674 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing