4IM7

Crystal structure of fructuronate reductase (ydfI) from E. coli CFT073 (EFI TARGET EFI-506389) complexed with NADH and D-mannonate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5282Protein solution was at 10 mg/mL containing 20 mM Tris (pH 7.5) and 100 mM NaCl. Mother liqueur contained 1.7 M ammonium sulfate, 0.085 M Hepes (pH 7.5), 1.7% PEG 400 and 15% glycerol, vapor diffusion, sitting drop, temperature 282K
Crystal Properties
Matthews coefficientSolvent content
359.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.49α = 90
b = 92.49β = 90
c = 136γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252012-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
11.93099.90.0911.4253597-327.297
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)
11.91.9599.90.6112.55

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)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 DIFFRACTIONMOLECULAR REPLACEMENT1.929.5512.025364753593267999.940.14960.14840.1728random23.6144
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]
-0.0825-0.08250.165
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15
f_angle_d1.105
f_chiral_restr0.072
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3758
Nucleic Acid Atoms
Solvent Atoms471
Heterogen Atoms62

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction