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Crystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans in complex with salicylate
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 3.29 62.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.273 α = 90 b = 86.977 β = 90 c = 167.626 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 2008-01-01 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 2.45 83.918 99.1 0.079 0.079 11.7 3.4 20120 20120 52.1
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 2.45 2.58 99.5 0.477 0.477 1.6 2.9 2913
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 2.45 30 20084 1022 98.54 0.1972 0.1933 0.192 0.2724 0.2693 RANDOM 45.3088
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] 2.48 2.7 -5.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_3_deg 17.988 r_dihedral_angle_4_deg 16.716 r_dihedral_angle_1_deg 7.283 r_scangle_it 3.761 r_scbond_it 2.424 r_angle_refined_deg 1.877 r_mcangle_it 1.631 r_mcbond_it 0.889 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_3_deg 17.988 r_dihedral_angle_4_deg 16.716 r_dihedral_angle_1_deg 7.283 r_scangle_it 3.761 r_scbond_it 2.424 r_angle_refined_deg 1.877 r_mcangle_it 1.631 r_mcbond_it 0.889 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2735 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 29
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection