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Crystal Structure and Biochemical Characterization of GDOsp, a Gentisate 1,2-Dioxygenase from Silicibacter Pomeroyi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D40 PDB ENTRY 2D40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 289 PEG3350,NaI, hanging drop, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.26 45.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.999 α = 90 b = 129.999 β = 90 c = 246.255 γ = 120
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 RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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 2.8 50 99.9 0.112 8.2 11.2 20056
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) 2.8 2.9 100 0.423 11.3 1989
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2D40 2.8 41.93 20042 1019 99.8 0.212 0.21 0.245 0.2179 RANDOM 34.718
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] 0.48 0.24 0.48 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.601 r_dihedral_angle_3_deg 16.581 r_dihedral_angle_4_deg 13.256 r_dihedral_angle_1_deg 5.323 r_mcangle_it 1.474 r_scangle_it 0.991 r_angle_refined_deg 0.979 r_mcbond_it 0.852 r_scbond_it 0.634 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.601 r_dihedral_angle_3_deg 16.581 r_dihedral_angle_4_deg 13.256 r_dihedral_angle_1_deg 5.323 r_mcangle_it 1.474 r_scangle_it 0.991 r_angle_refined_deg 0.979 r_mcbond_it 0.852 r_scbond_it 0.634 r_nbtor_refined 0.296 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.11 r_symmetry_hbond_refined 0.108 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5672 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction