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Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M21
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 2.23 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.329 α = 90 b = 126.09 β = 105.02 c = 92.967 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 CCD MARMOSAIC 225 mm CCD 2016-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
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 2.39 47.508 97 0.107 0.987 6.83 1.97 76541 -3 32.845
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 2.39 2.53 95.5 0.526 0.66 1.62
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 5M21 2.4 30 72005 3643 97.36 0.1818 0.1782 0.1784 0.2539 0.2541 RANDOM 29.821
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] -1.03 1.14 -1.25 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.961 r_dihedral_angle_4_deg 19.043 r_dihedral_angle_3_deg 15.889 r_dihedral_angle_1_deg 7.034 r_mcangle_it 2.806 r_scbond_it 2.198 r_mcbond_it 1.772 r_angle_refined_deg 1.545 r_chiral_restr 0.101 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.961 r_dihedral_angle_4_deg 19.043 r_dihedral_angle_3_deg 15.889 r_dihedral_angle_1_deg 7.034 r_mcangle_it 2.806 r_scbond_it 2.198 r_mcbond_it 1.772 r_angle_refined_deg 1.545 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15302 Nucleic Acid Atoms Solvent Atoms 677 Heterogen Atoms 4
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XSCALE data reduction REFMAC phasing