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Room Temperature X-ray structure of D-Xylose Isomerase complexed with 2Cd(2+) co-factors and d12-D-alpha-glucose in the cyclic form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.7 290 40mg/ml protein, 5mM CdCl2; 500mM d12-D-glucose, 30% (v/v) ammonium sulfate (sat.), batch, pH 7.7, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.79 55.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.196 α = 90 b = 99.43 β = 90 c = 102.986 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 293 IMAGE PLATE RIGAKU RAXIS IV++ Varimax mirrors 2009-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54
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 20 90 30084 27223 4 2
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 2 2.07 93.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1XIB 2 20 30084 27223 1507 91.2 0.1784 0.176 0.1514 0.2113 0.1794 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 3 3259
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.078 s_non_zero_chiral_vol 0.038 s_zero_chiral_vol 0.032 s_angle_d 0.022 s_from_restr_planes 0.0215 s_anti_bump_dis_restr 0.008 s_bond_d 0.006 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3053 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 14
Software Software Software Name Purpose CrystalClear data collection SHELX model building SHELXL-97 refinement CrystalClear data reduction CrystalClear data scaling SHELX phasing