4IP4

Crystal structure of l-fuconate dehydratase from Silicibacter sp. tm1040 liganded with Mg


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HXTpdb entry 2HXT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529325% PEG 3350, 0.1M Hepes, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.2545.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.051α = 90
b = 141.332β = 90
c = 59.778γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9A0.979NSLSX9A

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
12.12838.58899.754872948729

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 2HXT2.12838.5884872948729246399.750.14250.14250.14020.1834RANDOM
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_d13.326
f_angle_d1.051
f_chiral_restr0.074
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6594
Nucleic Acid Atoms
Solvent Atoms533
Heterogen Atoms32

Software

Software
Software NamePurpose
ADSCdata collection
BALBESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling