4DVO

Room-temperature joint X-ray/neutron structure of D-xylose isomerase in complex with 2Ni2+ and per-deuterated D-sorbitol at pH 5.9


NEUTRON DIFFRACTION - X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch5.9290apo-Xylose isomerase crystals were grown with AmSO4 as precipitant and 0.1 M MES at pH 5.9; they then were injected with Ni2+ salt up to the concentration of 5mM and D-sorbitol up to the concentration of 300mM, batch, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.7855.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.061α = 90
b = 99.428β = 90
c = 102.798γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11neutron293AREA DETECTORHe3-filled PSD2010-07-15MSINGLE WAVELENGTH
21x-ray293IMAGE PLATERIGAKU RAXIS IV++2010-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1NUCLEAR REACTOR2.422D19
2ROTATING ANODERIGAKU FR-E DW1.54

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1249.72930.1547.64305852
21.5529.997.50.0729.33.2268214
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)RedundancyNumber Unique Reflections (All)
122.10.4081.82.4
21.551.610.3472.62.66

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT22023058530162150191.80.190.190.214RANDOM
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
KeyRefinement Restraint Deviation
c_angle_deg0.92
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3054
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms15

Software

Software
Software NamePurpose
CNSrefinement
nCNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing