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Marine bacterial prolidase with promiscuous organophosphorus hydrolase activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZWO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2 M Ammonium sulfate, 5% PEG400, 100 mM MES pH6.5
Crystal Properties Matthews coefficient Solvent content 2.83 56.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.854 α = 90 b = 178.854 β = 90 c = 371.586 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 16M 2018-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97892 SSRF BL19U1
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 2.6 50 100 0.176 14.1 9.9 70044
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 2.6 2.69 99.9 0.851 2 9.8
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ZWO 2.61 44.53 66253 3493 99.73 0.226 0.2266 0.279 0.2785 RANDOM 72.136
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] 2.14 1.07 2.14 -6.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.824 r_dihedral_angle_3_deg 17.344 r_dihedral_angle_4_deg 16.595 r_long_range_B_refined 8.268 r_long_range_B_other 8.267 r_dihedral_angle_1_deg 6.804 r_mcangle_it 5.704 r_mcangle_other 5.704 r_scangle_other 5.379 r_mcbond_it 3.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.824 r_dihedral_angle_3_deg 17.344 r_dihedral_angle_4_deg 16.595 r_long_range_B_refined 8.268 r_long_range_B_other 8.267 r_dihedral_angle_1_deg 6.804 r_mcangle_it 5.704 r_mcangle_other 5.704 r_scangle_other 5.379 r_mcbond_it 3.609 r_mcbond_other 3.606 r_scbond_it 3.289 r_scbond_other 3.278 r_angle_refined_deg 0.995 r_angle_other_deg 0.749 r_chiral_restr 0.046 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14256 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing