3K4D

Crystal structure of E. coli beta-glucuronidase with the glucaro-d-lactam inhibitor bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K4APDB entry 3K4A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.428915% PEG 3350, 0.2 M Mg Acetate, 0.02% Sodium azide, 500 mM Glucaro-d-lactam, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4149.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.653α = 90
b = 76.971β = 124.98
c = 125.468γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-02-18MSINGLE 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
12.3935098.330.082751884
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)
12.3932.4993.90.4226.2

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 REPLACEMENTTHROUGHOUTPDB entry 3K4A2.39329.5750982250298.330.20610.204550.23682RANDOM71.57
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]
-1.890.381.640.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.466
r_dihedral_angle_3_deg19.192
r_dihedral_angle_4_deg18.761
r_dihedral_angle_1_deg10.975
r_scangle_it6.681
r_mcangle_it4.834
r_scbond_it4.055
r_mcbond_it2.626
r_rigid_bond_restr2.257
r_angle_refined_deg1.521
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.466
r_dihedral_angle_3_deg19.192
r_dihedral_angle_4_deg18.761
r_dihedral_angle_1_deg10.975
r_scangle_it6.681
r_mcangle_it4.834
r_scbond_it4.055
r_mcbond_it2.626
r_rigid_bond_restr2.257
r_angle_refined_deg1.521
r_chiral_restr0.121
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9552
Nucleic Acid Atoms
Solvent Atoms355
Heterogen Atoms26

Software

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