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Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 with 4-hydroxybenzoate bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 296 14% PEG 3350, 0.35 M MgCl2 and 0.1 M Mes
Crystal Properties Matthews coefficient Solvent content 2.17 43.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.782 α = 90 b = 124.869 β = 105.15 c = 92.371 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 2M 2016-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0000 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 29.856 97.7 0.117 0.994 8.86 4.32 130301 -3 30.103
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.11 88.9 0.583 0.846 2.45
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 MOLECULAR REPLACEMENT THROUGHOUT 4ZXA 1.99 29.8 123544 6614 98.56 0.1824 0.1793 0.1797 0.2419 0.2423 RANDOM 27.432
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] -1.85 -0.19 -1.04 2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.196 r_dihedral_angle_4_deg 20.406 r_dihedral_angle_3_deg 15.305 r_dihedral_angle_1_deg 7.043 r_mcangle_it 2.872 r_scbond_it 2.814 r_mcbond_it 2.035 r_angle_refined_deg 1.785 r_chiral_restr 0.12 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.196 r_dihedral_angle_4_deg 20.406 r_dihedral_angle_3_deg 15.305 r_dihedral_angle_1_deg 7.043 r_mcangle_it 2.872 r_scbond_it 2.814 r_mcbond_it 2.035 r_angle_refined_deg 1.785 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15386 Nucleic Acid Atoms Solvent Atoms 1141 Heterogen Atoms 44
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing