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Crystal structure of the E. coli xylulose kinase complexed with xylulose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 298 Drops containing equal volume of 26 mg/ml protein solution and precipitant solution comprising of 1.5
M ammonium sulfate, 50 mM sodium citrate, 1% w/v t-butanol, suspended over a 1 ml
reservoir containing the precipitant solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.37 48.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.883 α = 90 b = 112.605 β = 90 c = 143.073 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 2004-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 2.1 29.85 96.4 58656 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 30 89.88
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 2.1 29.85 56530 2278 96.4 0.204 0.201 0.263 0.3074 RANDOM 31.4
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] 1.22 -2.27 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.141 r_dihedral_angle_4_deg 22.7 r_dihedral_angle_3_deg 21.822 r_scangle_it 15.279 r_scbond_it 13.8 r_dihedral_angle_1_deg 10.056 r_mcangle_it 9.35 r_mcbond_it 8.482 r_angle_other_deg 4.313 r_mcbond_other 4.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.141 r_dihedral_angle_4_deg 22.7 r_dihedral_angle_3_deg 21.822 r_scangle_it 15.279 r_scbond_it 13.8 r_dihedral_angle_1_deg 10.056 r_mcangle_it 9.35 r_mcbond_it 8.482 r_angle_other_deg 4.313 r_mcbond_other 4.074 r_angle_refined_deg 1.332 r_chiral_restr 0.34 r_symmetry_vdw_other 0.337 r_nbd_other 0.313 r_symmetry_vdw_refined 0.302 r_nbd_refined 0.286 r_xyhbond_nbd_refined 0.268 r_xyhbond_nbd_other 0.256 r_symmetry_hbond_refined 0.211 r_nbtor_refined 0.201 r_nbtor_other 0.119 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7257 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction CNS phasing