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Crystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans in complex with gentisate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 277 8% PEG10000, pH 8.0, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.37 63.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.5 α = 90 b = 86.89 β = 90 c = 166.83 γ = 90
Symmetry Space Group I 2 2 2
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 MAR CCD 165 mm 2008-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8123 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 83.415 98.7 0.065 0.065 15 4.2 37295 37295 40.159
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 98 0.414 0.414 1.8 3.5 5337
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 FOURIER SYNTHESIS THROUGHOUT 2PHD 2 30 37276 1872 98.21 0.1606 0.1583 0.1606 0.2021 0.2024 RANDOM 31.8513
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] 0.75 1.86 -2.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.657 r_dihedral_angle_4_deg 20.869 r_dihedral_angle_3_deg 15.487 r_dihedral_angle_1_deg 6.694 r_scangle_it 3.773 r_scbond_it 2.455 r_angle_refined_deg 1.563 r_mcangle_it 1.349 r_mcbond_it 0.761 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.657 r_dihedral_angle_4_deg 20.869 r_dihedral_angle_3_deg 15.487 r_dihedral_angle_1_deg 6.694 r_scangle_it 3.773 r_scbond_it 2.455 r_angle_refined_deg 1.563 r_mcangle_it 1.349 r_mcbond_it 0.761 r_chiral_restr 0.117 r_bond_refined_d 0.017 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2848 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 36
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection