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Structure of E323L Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum in complex with putative O-O bond cleavage intermediate formed via in crystallo reaction with 4-sulfonyl catechol at low oxygen concentrations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IG9 PDB ID 2IG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 18% PEG8000, 0.1M Ca acetate, 0.1M Na cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.74 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.735 α = 90 b = 163.176 β = 90 c = 101.373 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 SBC-3 2007-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97903 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 55 92.4 0.052 0.052 19.22 4.1 240583 222399 -3
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 1.6 1.66 73.2 0.342 3.067 3.3 17442
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID 2IG9 1.6 24.2 211226 11135 92.41 0.17521 0.17401 0.1733 0.19767 RANDOM 19.045
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.277 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_3_deg 12.249 r_dihedral_angle_1_deg 6.704 r_scangle_it 2.715 r_scbond_it 1.769 r_angle_refined_deg 1.297 r_mcangle_it 1.078 r_mcbond_it 0.7 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.277 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_3_deg 12.249 r_dihedral_angle_1_deg 6.704 r_scangle_it 2.715 r_scbond_it 1.769 r_angle_refined_deg 1.297 r_mcangle_it 1.078 r_mcbond_it 0.7 r_nbtor_refined 0.304 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.197 r_symmetry_vdw_refined 0.177 r_metal_ion_refined 0.118 r_xyhbond_nbd_refined 0.11 r_symmetry_metal_ion_refined 0.097 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11596 Nucleic Acid Atoms Solvent Atoms 1393 Heterogen Atoms 71
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling