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Serum paraoxonase-1 by directed evolution at pH 6.5 in complex with 2-hydroxyquinoline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SRE PDB ENTRY 3SRE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 20% PEG3350, 0.2 M sodium bromide, 0.1 M Bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.99 69.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.544 α = 90 b = 93.544 β = 90 c = 144.621 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 CCD ADSC QUANTUM 315r 2009-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.979 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.19 46.77 100 0.113 0.094 30.5 14.3 33798 33798
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.24 100 0.621 0.598 5.95 14.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3SRE 2.19 46.77 32016 32016 1705 99.55 0.18432 0.18209 0.1793 0.22695 0.2215 RANDOM 30.583
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 r_dihedral_angle_2_deg 35.484 r_dihedral_angle_4_deg 27.776 r_dihedral_angle_3_deg 14.58 r_dihedral_angle_1_deg 8.917 r_scangle_it 6.046 r_scbond_it 3.879 r_mcangle_it 2.679 r_angle_refined_deg 2.196 r_mcbond_it 1.571 r_chiral_restr 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.484 r_dihedral_angle_4_deg 27.776 r_dihedral_angle_3_deg 14.58 r_dihedral_angle_1_deg 8.917 r_scangle_it 6.046 r_scbond_it 3.879 r_mcangle_it 2.679 r_angle_refined_deg 2.196 r_mcbond_it 1.571 r_chiral_restr 0.209 r_bond_refined_d 0.03 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2605 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling