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Crystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase from Streptococcus agalactiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PPW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 15% polyethylene glycol 10,000, 2% dioxane, and 0.1 M sodium citrate (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.234 α = 90 b = 87.968 β = 90 c = 90.295 γ = 90
Symmetry Space Group I 2 2 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 315 2011-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 50 100 28.6 6 14717
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2PPW 2 45.15 13926 737 99.05 0.18164 0.17942 0.22491 0.2155 RANDOM 27.179
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] -0.01 -0.05 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.777 r_dihedral_angle_4_deg 26.866 r_dihedral_angle_3_deg 11.378 r_dihedral_angle_1_deg 4.484 r_long_range_B_refined 2.839 r_long_range_B_other 2.741 r_scangle_other 1.426 r_mcangle_it 1.244 r_mcangle_other 1.243 r_angle_refined_deg 0.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.777 r_dihedral_angle_4_deg 26.866 r_dihedral_angle_3_deg 11.378 r_dihedral_angle_1_deg 4.484 r_long_range_B_refined 2.839 r_long_range_B_other 2.741 r_scangle_other 1.426 r_mcangle_it 1.244 r_mcangle_other 1.243 r_angle_refined_deg 0.934 r_scbond_it 0.822 r_scbond_other 0.821 r_mcbond_it 0.743 r_mcbond_other 0.742 r_angle_other_deg 0.72 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1656 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement