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Structure of phosphotriesterase mutant (S308L/Y309A) from Agrobacterium radiobacter with diethyl thiophosphate bound in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 20% PEG3350, 0.2M NANO3, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.06 59.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.134 α = 90 b = 109.134 β = 90 c = 63.428 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2013-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.5418
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 1.99 28.22 99.8 0.123 15.4 7.2 30260 30260
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 1.99 2.04 98.4 0.889 2.4 6.6 30260
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 (All) 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 2D2J 1.99 28.22 28317 28317 1510 98.33 0.20799 0.20799 0.20567 0.2157 0.25108 0.255 RANDOM 23.797
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] -0.01 -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.656 r_dihedral_angle_4_deg 16.485 r_dihedral_angle_3_deg 14.954 r_dihedral_angle_1_deg 6.223 r_long_range_B_refined 5.556 r_long_range_B_other 5.482 r_scangle_other 4.24 r_mcangle_it 3.023 r_mcangle_other 3.022 r_scbond_it 2.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.656 r_dihedral_angle_4_deg 16.485 r_dihedral_angle_3_deg 14.954 r_dihedral_angle_1_deg 6.223 r_long_range_B_refined 5.556 r_long_range_B_other 5.482 r_scangle_other 4.24 r_mcangle_it 3.023 r_mcangle_other 3.022 r_scbond_it 2.868 r_scbond_other 2.866 r_mcbond_it 2.07 r_mcbond_other 2.07 r_angle_refined_deg 2.036 r_angle_other_deg 0.947 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 2506 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 15
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction Aimless data scaling