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Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 in complex with methylhydroquinone
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 2.17 43.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.406 α = 90 b = 125.231 β = 102.55 c = 91.352 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 1.9 46.694 97.5 0.123 0.994 10.43 4.84 149371 -3 24.408
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 1.9 2.01 94.8 0.604 0.797 2.72
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 1.9 30 141943 7452 97.54 0.1628 0.1604 0.1606 0.2074 0.2079 RANDOM 21.792
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] -1.01 0.68 -0.39 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.759 r_dihedral_angle_4_deg 19.557 r_dihedral_angle_3_deg 13.952 r_dihedral_angle_1_deg 6.592 r_mcangle_it 1.696 r_scbond_it 1.66 r_angle_refined_deg 1.414 r_mcbond_it 1.073 r_chiral_restr 0.102 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.759 r_dihedral_angle_4_deg 19.557 r_dihedral_angle_3_deg 13.952 r_dihedral_angle_1_deg 6.592 r_mcangle_it 1.696 r_scbond_it 1.66 r_angle_refined_deg 1.414 r_mcbond_it 1.073 r_chiral_restr 0.102 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15307 Nucleic Acid Atoms Solvent Atoms 2035 Heterogen Atoms 38
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing