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Room Temperature X-ray Structure of D-Xylose Isomerase in complex with 0.6Ni2+ cation bound in M2 metal binding site at pH=5.8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch crystallization 5.8 280 apo-XI was crystallized with ammonium sulfate as precipitant; 0.2mM Ni2+ salt was added to make the complex, pH 5.8, batch crystallization, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.42 56.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.9 α = 90 b = 99.63 β = 90 c = 102.84 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 2010-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
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 1.85 31.6 94.5 0.059 14 3.89 39184 4 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 67.9 0.258 2.4 1.61
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 AB INITIO PHASING FREE R NONE 1.85 10 38893 38893 1958 93.5 0.1734 0.1706 0.1567 0.2175 0.1977 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 3279.6
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.083 s_non_zero_chiral_vol 0.049 s_zero_chiral_vol 0.038 s_angle_d 0.024 s_from_restr_planes 0.0224 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 269 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection SHELX model building SHELXL-97 refinement d*TREK data reduction d*TREK data scaling SHELX phasing