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Room temperature X-ray structure of D-xylose isomerase in complex with two Mg2+ ions and L-ribose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 7.7 291 30% ammonium sulfate, 0.1M HEPES pH 7.7, batch, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.78 55.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.922 α = 90 b = 99.561 β = 90 c = 103.051 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 291 IMAGE PLATE RIGAKU RAXIS IV++ 2013-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 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 1.55 40 85 69155 58816 4 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 AB INITIO FREE R NONE 1.55 20 66366 3327 94.8 0.1595 0.1581 0.1552 0.1839 0.1798 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 5 3316.5
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.082 s_similar_adp_cmpnt 0.069 s_zero_chiral_vol 0.057 s_angle_d 0.028 s_from_restr_planes 0.0228 s_anti_bump_dis_restr 0.022 s_bond_d 0.011 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 255 Heterogen Atoms 12
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing SHELXL-97 refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing