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Crystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase complexed with a tartrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.0 M ammonium sulfate, 0.2 M potassium sodium tartrate, and 0.1 M sodium citrate (pH 5.6)
Crystal Properties Matthews coefficient Solvent content 2.84 56.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.955 α = 90 b = 92.955 β = 90 c = 129.35 γ = 90
Symmetry Space Group P 41 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 210 2011-12-09 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 1.55 50 99.4 47.3 7.5 82052
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 MOLECULAR REPLACEMENT THROUGHOUT 4U8E 1.55 36.08 77602 4096 98.93 0.19892 0.19825 0.21125 0.2085 RANDOM 17.396
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] 0.43 0.43 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.727 r_dihedral_angle_4_deg 18.235 r_dihedral_angle_3_deg 11.022 r_dihedral_angle_1_deg 4.24 r_angle_refined_deg 0.932 r_chiral_restr 0.071 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.727 r_dihedral_angle_4_deg 18.235 r_dihedral_angle_3_deg 11.022 r_dihedral_angle_1_deg 4.24 r_angle_refined_deg 0.932 r_chiral_restr 0.071 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3313 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement