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Crystal structure of member of Glyoxalase/bleomycin resistance protein/dioxygenase superfamily from Sphaerobacter thermophilus DSM 20745
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 Ammonium sulfate 1.5 M, Tris 0.1 M, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.68 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.883 α = 90 b = 71.023 β = 90 c = 86.698 γ = 90
Symmetry Space Group P 21 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 315r mirrors 2012-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.45 86 99 0.085 40 11.3 116629 115474 2 2 29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 99.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.45 26.59 2 114882 109125 5757 98.41 0.1391 0.13691 0.1447 0.18271 0.1826 RANDOM 23.861
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] 0.78 -0.61 -0.16
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.755 r_dihedral_angle_2_deg 36.925 r_dihedral_angle_4_deg 20.463 r_sphericity_bonded 15.829 r_dihedral_angle_3_deg 12.87 r_rigid_bond_restr 7.333 r_dihedral_angle_1_deg 6.396 r_angle_other_deg 3.959 r_angle_refined_deg 2.031 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.755 r_dihedral_angle_2_deg 36.925 r_dihedral_angle_4_deg 20.463 r_sphericity_bonded 15.829 r_dihedral_angle_3_deg 12.87 r_rigid_bond_restr 7.333 r_dihedral_angle_1_deg 6.396 r_angle_other_deg 3.959 r_angle_refined_deg 2.031 r_chiral_restr 0.132 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_gen_planes_other 0.011 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4008 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 12
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing SHELX model building MLPHARE phasing DM model building ARP model building WARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing DM phasing