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Joint X-ray and neutron structure of Streptomyces rubiginosus D-xylose isomerase in complex with two Ni2+ ions and linear L-arabinose
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 7.7 291 30% ammonium sulfate, 0.1 M HEPES pH 7.7, batch, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.79 55.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.19 α = 90 b = 99.67 β = 90 c = 102.94 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++ OSMIC VARIMAX 2012-03-20 M SINGLE WAVELENGTH 2 1 neutron 291 AREA DETECTOR 3He position sensitive detector 2011-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 2 NUCLEAR REACTOR 2.422 D19
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.6 34.23 99.5 0.076 8.7 3.5 64130 2 10.1 2 1.8 71.6 81.5 0.12 10.5 2.7 36814 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.65 0.383 2.4 3.3 1.8 1.9 0.49 1.5 1.9
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.8 20 2 36814 28443 1446 0.166 0.166 0.166 0.179 random 29
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]
RMS Deviations Key Refinement Restraint Deviation x_torsion_deg 17.8 x_angle_deg 0.9 x_torsion_impr_deg 0.84 x_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3054 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 13
Software Software Software Name Purpose nCNS refinement d*TREK data scaling HKL-3000 data reduction RETREAT data reduction HKL-3000 data scaling RETREAT data scaling CNS phasing