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Crystal structure of Catechol 1,2-dioxygenase from Burkholderia vietnamiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DMH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 Rigaku Reagents Screen JCSG+ well D6: 0.2 M Magnesium Chloride, 20% PEG 8000, 0.1 M Tris pH 8.5; 0.4 uL screen : 0.4 uL BuviA.00117.a.B1.PS02511 at 21.4 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.78 55.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.41 α = 90 b = 55.86 β = 116.3 c = 85.69 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 CCD MARMOSAIC 300 mm CCD 2016-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 40.513 99.5 0.052 0.999 16.72 4.15 72445 -3 22.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 99.8 0.577 0.759 2.48
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1DMH 1.75 40.513 1.34 72441 1995 99.68 0.1779 0.177 0.1807 0.2101 0.2097 32.0597
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 10.417 f_angle_d 0.818 f_chiral_restr 0.053 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4577 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms 113
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing XDS data reduction