3LPG

Structure of E. coli beta-Glucuronidase bound with a novel, potent inhibitor 3-(2-fluorophenyl)-1-(2-hydroxyethyl)-1-((6-methyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)urea


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K4D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.428915% PEG 3350, 0.2 M MgAcetate, 0.02% sodium azide, 5 mM 3-(2-fluorophenyl)-1-(2-hydroxyethyl)-1-((6-methyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)urea, pH 7.4, vapor diffusion, hanging drop, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4148.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.814α = 90
b = 76.934β = 124.75
c = 125.81γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

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
12.42530.85989.540.136926.63.944902
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.4252.477774.53.92260

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENT3K4D2.42530.8590.144902228789.540.2060.2040.24670.727
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]
-17.7632.66521.641-7.91
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.352
f_angle_d1.023
f_chiral_restr0.088
f_plane_restr0.007
f_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9655
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms54

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
X-GENdata reduction
X-GENdata scaling