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Structural basis for natural lactonase and promiscuous phosphotriesterase activities
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPM PDB ENTRY 1DPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 50MM TRIS-HCL PH 8, 15-18% PEG 8000, 0.1MM COCL2
Crystal Properties Matthews coefficient Solvent content 2.5 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.16 α = 90 b = 104.82 β = 90 c = 155.36 γ = 90
Symmetry Space Group P 21 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 MARRESEARCH 2006-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 2.59 44.9 95.3 0.16 11.69 3.6 85611 2
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 (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 1DPM 2.6 44.9 42121 2234 99.4 0.225 0.222 0.2223 0.282 0.2803 RANDOM 38.8
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] 0.87 -0.2 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.472 r_dihedral_angle_3_deg 18.412 r_dihedral_angle_4_deg 13.899 r_dihedral_angle_1_deg 5.856 r_angle_refined_deg 1.061 r_mcangle_it 0.423 r_scangle_it 0.409 r_nbtor_refined 0.301 r_scbond_it 0.249 r_mcbond_it 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.472 r_dihedral_angle_3_deg 18.412 r_dihedral_angle_4_deg 13.899 r_dihedral_angle_1_deg 5.856 r_angle_refined_deg 1.061 r_mcangle_it 0.423 r_scangle_it 0.409 r_nbtor_refined 0.301 r_scbond_it 0.249 r_mcbond_it 0.247 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.168 r_symmetry_vdw_refined 0.164 r_symmetry_hbond_refined 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10052 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing