3KBW

Room temperature X-ray mixed-metal structure of D-Xylose Isomerase in complex with Ni(2+) and Mg(2+) co-factors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch7.729040mg/ml protein, 2mM NiCl2, 2mM MgCl2, 30% (v/v) ammonium sulfate (sat.), pH 7.7, batch, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.7855.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.972α = 90
b = 99.701β = 90
c = 102.855γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS IV++2008-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.61080628675001442
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6595

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONAB INITIOFREE R1.61062867313198.90.12160.11920.1665RANDOM
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 MethodRefinement High ResolutionRefinement Low Resolution
33338
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.114
s_non_zero_chiral_vol0.063
s_similar_adp_cmpnt0.061
s_zero_chiral_vol0.047
s_angle_d0.029
s_from_restr_planes0.0232
s_anti_bump_dis_restr0.015
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3053
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms2

Software

Software
Software NamePurpose
CrystalCleardata collection
SHELXmodel building
SHELXL-97refinement
CrystalCleardata reduction
CrystalCleardata scaling
SHELXphasing