2GUB

Crystal Structure of Metal Free D-Xylose Isomerase.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES8279Crystallization from solution containing metal free enzyme at 20 mg/ml, 0.8M AmSO4, 2mM Pipes. Crystallization occurred over 2 day period in sealed tubes., pH 8.0, SMALL TUBES, temperature 279K
Crystal Properties
Matthews coefficientSolvent content
2.7755.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.8α = 90
b = 99.5β = 90
c = 102.8γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray279AREA DETECTORSIEMENS-NICOLET X100focussing nickel mirrors1995-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.870.710.834056921
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.986.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1XIB without metal ions and solvent1.870.714056940237212193.790.161240.159580.19327RANDOM17.994
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]
-0.380.20.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.465
r_dihedral_angle_4_deg16.095
r_dihedral_angle_3_deg14.331
r_dihedral_angle_1_deg5.304
r_scangle_it5.192
r_scbond_it3.281
r_mcangle_it1.802
r_angle_refined_deg1.739
r_mcbond_it1.235
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.465
r_dihedral_angle_4_deg16.095
r_dihedral_angle_3_deg14.331
r_dihedral_angle_1_deg5.304
r_scangle_it5.192
r_scbond_it3.281
r_mcangle_it1.802
r_angle_refined_deg1.739
r_mcbond_it1.235
r_nbtor_refined0.311
r_nbd_refined0.2
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.182
r_xyhbond_nbd_refined0.161
r_chiral_restr0.152
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3033
Nucleic Acid Atoms
Solvent Atoms374
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DATCOLdata reduction
XDSdata scaling
XTALVIEWrefinement