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Structure of phosphotriesterase mutant (S308L/Y309A) from Agrobacterium radiobacter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D2J PDB ENTRY 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 2.97 58.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.996 α = 90 b = 108.996 β = 90 c = 61.774 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 Mirrors 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 1.987 29.355 99.8 0.122 20.2 10.8 29386 29366
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 99.8 0.75 4 9.9 29386
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 PDB ENTRY 2D2J 1.99 29.355 27872 27872 1494 99.82 0.1582 0.1582 0.15668 0.1731 0.18672 0.1958 RANDOM 19.483
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] -0.09 -0.09 -0.09 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.965 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_1_deg 6.478 r_long_range_B_refined 5.152 r_long_range_B_other 5.112 r_scangle_other 4.188 r_scbond_it 2.786 r_scbond_other 2.784 r_mcangle_it 2.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.965 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_1_deg 6.478 r_long_range_B_refined 5.152 r_long_range_B_other 5.112 r_scangle_other 4.188 r_scbond_it 2.786 r_scbond_other 2.784 r_mcangle_it 2.378 r_mcangle_other 2.378 r_angle_refined_deg 2.084 r_mcbond_it 1.755 r_mcbond_other 1.753 r_angle_other_deg 1.309 r_chiral_restr 0.132 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 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 155 Heterogen Atoms 6
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction Aimless data scaling