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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 2VC5 PDB ENTRY 2VC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 TRIS-HCL 50MM PH 8, 15-18% W/V PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.5 40.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.383 α = 90 b = 104.124 β = 90 c = 153.051 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.05 61.66 99.9 0.13 13.66 7.25 141906 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.15 92.8 7.1
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 2VC5 2.05 61.66 82756 4370 99.9 0.239 0.237 0.2384 0.287 0.288 RANDOM 28.86
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] 0.6 -0.17 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.315 r_dihedral_angle_3_deg 17.318 r_dihedral_angle_4_deg 16.479 r_dihedral_angle_1_deg 6.708 r_angle_refined_deg 1.119 r_scangle_it 0.438 r_mcangle_it 0.42 r_nbtor_refined 0.297 r_scbond_it 0.286 r_mcbond_it 0.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.315 r_dihedral_angle_3_deg 17.318 r_dihedral_angle_4_deg 16.479 r_dihedral_angle_1_deg 6.708 r_angle_refined_deg 1.119 r_scangle_it 0.438 r_mcangle_it 0.42 r_nbtor_refined 0.297 r_scbond_it 0.286 r_mcbond_it 0.257 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.124 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.104 r_xyhbond_nbd_refined 0.088 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 760 Heterogen Atoms 348
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing