3KBN

Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors and d12-D-glucose in the linear form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XIB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.729040mg/ml protein, 5mM NiCl2, 500mM d12-D-glucose 30% (v/v) ammonium sulfate (sat.), pH 7.7, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.7855.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.007α = 90
b = 99.669β = 90
c = 102.862γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS IV++2009-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.54

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
11.532085722686165542
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.5893.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1XIB1.53207226861655361999.20.14060.1380.1815RANDOM
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
53360.5
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.09
s_non_zero_chiral_vol0.068
s_similar_adp_cmpnt0.061
s_zero_chiral_vol0.055
s_angle_d0.028
s_from_restr_planes0.0232
s_anti_bump_dis_restr0.018
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3053
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms15

Software

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