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Room-temperature X-ray structure of D-Xylose Isomerase in complex with 2Mg2+ ions and xylitol at pH 7.7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 7.7 290 apo-XI crystals were grown with AmSO4 by batch; to obtain the complex Mg2+ was injected into drops containing crystals up to concentration 5 mM; subsequently, xylitol was injected up to concentration of 100 mM, pH 7.7, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.79 α = 90 b = 99.62 β = 90 c = 102.83 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++ 2009-02-25 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 10 94 31224 29332 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 2.11 95
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FREE R 2 10 31224 29332 1580 95.8 0.148 0.144 0.1412 0.1391 0.1997 0.1896 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 1 3284
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.079 s_non_zero_chiral_vol 0.044 s_zero_chiral_vol 0.035 s_from_restr_planes 0.0232 s_angle_d 0.023 s_anti_bump_dis_restr 0.01 s_bond_d 0.007 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 228 Heterogen Atoms 12
Software Software Software Name Purpose CrystalClear data collection PHASER phasing SHELXL-97 refinement d*TREK data reduction SCALA data scaling