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Crystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Iron 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 25% (w/v) 4000, 0.2M CaCl2, 0.1M Tris 8.5, BumuA.00107.d.A2.PW32075 at 21.7 mg/mL. plate Liu-S-128 B7. Protein prepared in the presence of FeCl2. Puck: PSL-1602, Cryo: 32% (w/v) 4000, 0.2M CaCl2, 0.1M Tris 8.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.467 α = 90 b = 52.327 β = 92.5 c = 120.396 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 1.42 120.28 99.9 0.09 0.098 0.039 0.998 9.8 6.5 135545
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 1.42 1.46 99.9 1.143 1.24 0.475 0.786 6.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.42 57.68 1.33 135355 6709 99.77 0.145 0.1435 0.1538 0.1727 0.1791
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 12.853 f_angle_d 0.807 f_chiral_restr 0.075 f_plane_restr 0.012 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4687 Nucleic Acid Atoms Solvent Atoms 918 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing