8EYM

CRYSTAL STRUCTURE OF NAGB-II PHOSPHOSUGAR ISOMERASE FROM SHEWANELLA DENITRIFICANS OS217 IN COMPLEX WITH GLUCITOLAMINE-6-PHOSPHATE AND N-ACETYLGLUCOSAMINE-6-PHOSPHATE AT 2.31 A RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSdNagBII-GlcNol6P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52910.2 M MgCl2, 0.25 M Tris-HCl pH 8.5, 30% w/v PEG 4000. Crystals containing GlcNol6P and GlcNAc6P grew in the presence of 1 mM GlcNAc6P and were soaked in the crystallization drop with 1 mM GlcNol6P five minutes before freezing for data collection.
Crystal Properties
Matthews coefficientSolvent content
1.8935

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.181α = 90
b = 80.237β = 90
c = 91.508γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2018-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5406

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.3139.7594.410.94536.14.622873
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.312.350.223

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUESdNagBII-GlcNol6P2.31139.7460.932287399894.410.18770.18560.2333
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
f_dihedral_angle_d6.013
f_angle_d1.056
f_chiral_restr0.078
f_bond_d0.008
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4708
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms70

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing