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Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F1X PDB ENTRY 1F1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 292 18% PEG8000, 0.2 M calcium acetate, 0.1 M
sodium cacodylate. Prior to freezing in liquid nitrogen, crystals were sequentially transferred into mother liquor solutions containing 5, 10, 15, and then 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.25 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.678 α = 90 b = 153.022 β = 90 c = 96.389 γ = 90
Symmetry Space Group P 21 21 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 NOIR-1 2006-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 ALS 4.2.2
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 1.95 52.7 87.8 0.095 5.4 2.08 105058
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 1.95 2.02 91.6 0.379 1.9 2.16
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1F1X 1.95 52.7 104994 104994 5277 87.8 0.185 0.1888 0.245 0.2477 32.59
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.727 r_dihedral_angle_4_deg 18.432 r_dihedral_angle_3_deg 14.294 r_dihedral_angle_1_deg 7.34 r_scangle_it 3.467 r_scbond_it 2.55 r_angle_refined_deg 1.671 r_mcangle_it 1.36 r_mcbond_it 1.112 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.727 r_dihedral_angle_4_deg 18.432 r_dihedral_angle_3_deg 14.294 r_dihedral_angle_1_deg 7.34 r_scangle_it 3.467 r_scbond_it 2.55 r_angle_refined_deg 1.671 r_mcangle_it 1.36 r_mcbond_it 1.112 r_nbtor_refined 0.308 r_nbd_refined 0.21 r_symmetry_metal_ion_refined 0.195 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.122 r_metal_ion_refined 0.096 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11600 Nucleic Acid Atoms Solvent Atoms 1042 Heterogen Atoms 139
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling CCP4 phasing