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Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 7.7 290 40mg/ml protein, 5mM NiCl2, 30% (v/v) ammonium sulfate (sat.), pH 7.7, batch, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.99 α = 90 b = 99.47 β = 90 c = 102.96 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++ 2008-10-03 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 1.8 20 92 44836 41073 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 1.8 1.88 95
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 20 44836 2235 99.7 0.1836 0.1811 0.1581 0.2231 0.1863 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 3275.5
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.074 s_non_zero_chiral_vol 0.052 s_zero_chiral_vol 0.042 s_angle_d 0.023 s_from_restr_planes 0.0224 s_anti_bump_dis_restr 0.014 s_bond_d 0.008 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 224 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection SHELX model building SHELXL-97 refinement CrystalClear data reduction CrystalClear data scaling SHELX phasing