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Crystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Zinc bound, P1 form)
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 4.6 291 20% 3350, 0.5M NaCl, 0.1M NaAc 4.6, BumuA.00107.d.A2.PW32075 at 21.7 mg/mL. plate 14238 well B2 drop 2. Protein was prepared in the presence if ZnCl2. Puck: PSL-1607, Cryo: 20% (v/v) PEG 200 + 80% (v/v) crystallant
Crystal Properties Matthews coefficient Solvent content 2.5 50.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.97 α = 106.04 b = 86.27 β = 96.74 c = 110.161 γ = 113.15
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 1.71 102.35 96.4 0.066 0.078 0.041 0.998 10.1 3.5 278593
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 1.71 1.75 95.8 0.709 0.836 0.439 0.632 3.6
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 1.71 51.99 1.96 278542 14078 96.39 0.1522 0.1506 0.1587 0.183 0.1894
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 13.449 f_angle_d 0.862 f_chiral_restr 0.053 f_plane_restr 0.009 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18792 Nucleic Acid Atoms Solvent Atoms 2520 Heterogen Atoms 566
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing