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Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EBR 3ebr, 2oq1, 3bal, 3cjx experimental model PDB 2OQ1 3ebr, 2oq1, 3bal, 3cjx experimental model PDB 3BAL 3ebr, 2oq1, 3bal, 3cjx experimental model PDB 3CJX 3ebr, 2oq1, 3bal, 3cjx
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Protein solution: protein concentration = 5 mg/ml in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM beta-mercaptoethanol. Chymotrypsin was added in a 1:50 mass-ratio prior to setting up hanging-drop crystallisation trials.
Well solution: 10 % w/v PEG 1k and 10 % PEG 10k (Molecular Dimensions Structure Screen 2, condition 46).
Crystal Properties Matthews coefficient Solvent content 2.48 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.557 α = 90 b = 82.557 β = 90 c = 114.008 γ = 120
Symmetry Space Group P 65 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 2013-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.072 ESRF BM14
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 2.2 57 86.3 0.136 12.6 9.8 10549
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) 1 2.2 2.3 49.4 0.619 3.1 7.1
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 3ebr, 2oq1, 3bal, 3cjx 2.2 71.5 10021 512 86.17 0.17564 0.17342 0.1708 0.21758 0.2202 RANDOM 29.697
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] -0.7 -0.35 -0.7 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.018 r_dihedral_angle_3_deg 19.201 r_dihedral_angle_4_deg 18.956 r_dihedral_angle_1_deg 7.77 r_angle_refined_deg 2.008 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.018 r_dihedral_angle_3_deg 19.201 r_dihedral_angle_4_deg 18.956 r_dihedral_angle_1_deg 7.77 r_angle_refined_deg 2.008 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1234 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement BALBES phasing MOLREP phasing ARP model building