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Crystal structure of Glyoxalase/bleomycin resistance protein/dioxygenase from Conexibacter woesei DSM 14684
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2M MgCl2, 0.1M This-Cl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.17 43.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.943 α = 90 b = 58.943 β = 90 c = 164.99 γ = 90
Symmetry Space Group P 43 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 ADSC QUANTUM 210r 2012-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97931 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.56 50 97.7 0.115 24.9 7.9 42532 41562 -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 1.56 1.57 99.4 0.939 1.8 5.2 1044
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.56 37.2 41178 41178 2075 96.95 0.156 0.156 0.1543 0.1683 0.1869 0.1952 RANDOM 16.9125
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] -0.07 -0.07 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.318 r_sphericity_free 24.996 r_dihedral_angle_3_deg 14.187 r_sphericity_bonded 10.863 r_dihedral_angle_4_deg 10.625 r_dihedral_angle_1_deg 5.767 r_rigid_bond_restr 2.541 r_angle_refined_deg 1.362 r_chiral_restr 0.099 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.318 r_sphericity_free 24.996 r_dihedral_angle_3_deg 14.187 r_sphericity_bonded 10.863 r_dihedral_angle_4_deg 10.625 r_dihedral_angle_1_deg 5.767 r_rigid_bond_restr 2.541 r_angle_refined_deg 1.362 r_chiral_restr 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2154 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MLPHARE phasing DM phasing SHELXDE phasing ARP/wARP model building RESOLVE phasing Coot model building