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Engineering of organophosphate hydrolase by computational design and directed evolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FKW PDB ENTRY 1FKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 0.1 M Tris-HCl, 0.2 M calcium acetate, 20% PEG3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.17 43.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.391 α = 90 b = 77.592 β = 90 c = 94.972 γ = 90
Symmetry Space Group P 2 21 21
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 210 2010-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.35 50 98 0.065 31.3 10.1 15204 14900
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 91.4 0.303 5.4 5 1332
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 1FKW 2.35 42.4 14404 14116 755 98 0.1925 0.18949 0.1935 0.24993 0.2509 RANDOM 31.089
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] -0.06 -0.1 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.139 r_dihedral_angle_3_deg 16.137 r_dihedral_angle_4_deg 14.436 r_dihedral_angle_1_deg 6.736 r_scangle_it 1.978 r_scbond_it 1.175 r_angle_refined_deg 1.122 r_mcangle_it 0.703 r_mcbond_it 0.358 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.139 r_dihedral_angle_3_deg 16.137 r_dihedral_angle_4_deg 14.436 r_dihedral_angle_1_deg 6.736 r_scangle_it 1.978 r_scbond_it 1.175 r_angle_refined_deg 1.122 r_mcangle_it 0.703 r_mcbond_it 0.358 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 2796 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 5
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling