7PR6

Crystal structure of E. coli beta-glucuronidase in complex with covalent inhibitor ME727


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K46 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1 M Bis-Tris propane pH 7.5, 20% (w/v) PEG 3350, 0.2 M NaNO3
Crystal Properties
Matthews coefficientSolvent content
2.4449.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.8α = 90
b = 76.58β = 125.01
c = 125.74γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97933DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.9947.7697.30.1390.0830.9836.53.986916
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.0498.71.6950.9830.3340.83.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3k461.9947.80386915433396.8930.2230.22090.263148.325
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]
-1.766-0.2831.5720.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.678
r_dihedral_angle_4_deg15.514
r_dihedral_angle_3_deg14.33
r_dihedral_angle_1_deg8.092
r_lrange_it5.012
r_lrange_other4.98
r_scangle_it3.637
r_scangle_other3.636
r_mcangle_it3.06
r_mcangle_other3.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.678
r_dihedral_angle_4_deg15.514
r_dihedral_angle_3_deg14.33
r_dihedral_angle_1_deg8.092
r_lrange_it5.012
r_lrange_other4.98
r_scangle_it3.637
r_scangle_other3.636
r_mcangle_it3.06
r_mcangle_other3.06
r_angle_other_deg2.368
r_scbond_it2.321
r_scbond_other2.321
r_mcbond_it2.005
r_mcbond_other2.005
r_angle_refined_deg1.716
r_symmetry_nbd_refined0.281
r_nbd_other0.273
r_symmetry_nbd_other0.226
r_nbd_refined0.202
r_symmetry_xyhbond_nbd_refined0.184
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.162
r_chiral_restr0.079
r_symmetry_nbtor_other0.074
r_symmetry_xyhbond_nbd_other0.064
r_bond_other_d0.035
r_gen_planes_other0.016
r_bond_refined_d0.012
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9566
Nucleic Acid Atoms
Solvent Atoms469
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing