Navigation Tabs Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CWH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.7 293 50MM HEPES, 40% v/v (NH4)2SO4 (sat.), protein 40 MG/ML, PH=7.7, BATCH METHOD, APO-XI CRYSTALS WERE WITH 5mM CDCL2 SALT, 0.5M PER-DEUTERATED D-GLUCOSE IN D2O, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.196 α = 90 b = 99.43 β = 90 c = 102.986 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 neutron 293 AREA DETECTOR POSITION-SENSITIVE HE3 NEUTRON DETECTOR 2009-04-05 M SINGLE WAVELENGTH 2 1 x-ray 293 IMAGE PLATE RIGAKU RAXIS IV++ 2009-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR 2.422 D19 2 ROTATING ANODE RIGAKU FR-E DW 1.54
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 2 20 72 28961 20875 2 1.4
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 2 2.1 1.3 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 R-Free R-Free Selection Details Mean Isotropic B NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2 20 2.5 28961 20875 926 0.188 0.211 X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2 20 2.5 1430 0.173 0.194 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]
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.454 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3054 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 14
Software Software Software Name Purpose nCNS refinement RETREAT data reduction RETREAT data scaling nCNS phasing
