3E84

Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K1EPDB ENTRY 1K1E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529830% w/v polyethelene glycol (PEG) 4,000, 0.1 M Tris HCl pH 8.5, 0.2 M sodium acetate, 10 mM magnesium chloride and 50 mM sodium tungstate., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2645.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.086α = 90
b = 107.336β = 90
c = 75.31γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2005-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.855099.60.06415.75.2574532219.5
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)
11.851.9299.80.5062.255662

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTPDB ENTRY 1K1E1.8521.9261.9257417550298.230.1780.1760.218RANDOM27.393
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]
2.254-0.654-2.447
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.871
f_angle_d1.245
f_chiral_restr0.087
f_bond_d0.011
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5180
Nucleic Acid Atoms
Solvent Atoms512
Heterogen Atoms56

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOLREPphasing