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Crystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Iron and 4,5-dichloro-1,2-catechol bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UMH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 20% 4000, 0.2M CaCl2, 0.1M Tris 8.5 , BumuA.00107.d.A2.PW32075 at 21.7 mg/mL. plate Liu-S-128 A5. Overnight soak in 20mM 4,5-dichloro-1,2-catechol (45C) supplemented with 5mM FeCl2. Partial 45C occupancy which was modeled as the enol form. Puck: PSL-1902, Cryo: 32% (w/v) 4000, 0.2M CaCl2, 0.1M Tris 8.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.393 α = 90 b = 52.306 β = 92.5 c = 120.402 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 XE 9M 2024-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.62 120.29 99.9 0.102 0.111 0.045 0.998 10.4 6.2 91411
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.66 99.9 1.308 1.426 0.56 0.787 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.62 52.89 1.33 91343 4660 99.82 0.158 0.1567 0.1831 0.1842
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 f_dihedral_angle_d 13.547 f_angle_d 0.988 f_chiral_restr 0.059 f_plane_restr 0.012 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4691 Nucleic Acid Atoms Solvent Atoms 837 Heterogen Atoms 93
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing