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Structure of dehydrated D-xylose isomerase from streptomyces rubiginosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIG PDB entry 1XIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 278 6mM Tris-HCl, 33mg/ml crystalline suspension, 0.91M ammonium sulfate, 1mM magnesium sulfate (Hampton Research Ltd.); Soaked in xylitol solution, pH 7.0, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.37 48.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.853 α = 90 b = 87.65 β = 90 c = 94.531 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 293 IMAGE PLATE STOE Xenocs multilayer optics 2007-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER
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 2 94.49 98.3 0.137 8.1 4 51870 51870 16.836
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1XIG 2 38.35 51870 2771 97.89 0.16254 0.16018 0.1633 0.2064 0.2097 RANDOM 14.967
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] -0.3 0.24 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.401 r_dihedral_angle_4_deg 20.119 r_dihedral_angle_3_deg 15.249 r_dihedral_angle_1_deg 5.645 r_scangle_it 2.736 r_mcangle_it 2.11 r_scbond_it 1.744 r_angle_refined_deg 1.615 r_mcbond_it 1.397 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.401 r_dihedral_angle_4_deg 20.119 r_dihedral_angle_3_deg 15.249 r_dihedral_angle_1_deg 5.645 r_scangle_it 2.736 r_mcangle_it 2.11 r_scbond_it 1.744 r_angle_refined_deg 1.615 r_mcbond_it 1.397 r_nbtor_refined 0.301 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.15 r_metal_ion_refined 0.135 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6062 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 24
Software Software Software Name Purpose STOE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling