3LPF

Structure of E. coli beta-Glucuronidase bound with a novel, potent inhibitor 1-((6,7-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)-1-(2-hydroxyethyl)-3-(3-methoxyphenyl)thiourea


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, 1mM 1-((6,7-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)-1-(2-hydroxyethyl)-3-(3-methoxyphenyl)thiourea, pH 7.4, vapor diffusion, hanging drop, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4349.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.058α = 90
b = 77.409β = 124.66
c = 126.152γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-BM

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
12.265096.90.12813.76.859357
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)
2.32.3478.90.46552398

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3K4D2.265059262290894.620.2110.2090.249RANDOM71.303
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]
-2.05-0.161.590.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.839
r_dihedral_angle_3_deg19.389
r_dihedral_angle_4_deg18.955
r_dihedral_angle_1_deg10.655
r_scangle_it5.869
r_mcangle_it4.517
r_scbond_it3.497
r_mcbond_it2.459
r_rigid_bond_restr2.182
r_angle_refined_deg1.594
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.839
r_dihedral_angle_3_deg19.389
r_dihedral_angle_4_deg18.955
r_dihedral_angle_1_deg10.655
r_scangle_it5.869
r_mcangle_it4.517
r_scbond_it3.497
r_mcbond_it2.459
r_rigid_bond_restr2.182
r_angle_refined_deg1.594
r_chiral_restr0.138
r_bond_refined_d0.011
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9644
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms58

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling