8OHX

Crystal structure of Beta-glucuronidase from Escherichia coli in complex with siastatin B derived inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7PR6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M Bis-Tris propane pH 7.5, 20% (w/v) PEG 3350, 0.2 M NaNO3
Crystal Properties
Matthews coefficientSolvent content
2.4449.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.281α = 90
b = 76.711β = 102.01
c = 141.018γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979500DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.9567.0498.40.9978.14.194487
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.980.717

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.9561.83594471464498.2290.2240.22060.284749.837
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]
-1.065-0.7354.979-3.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.386
r_dihedral_angle_3_deg16.886
r_dihedral_angle_4_deg14.877
r_dihedral_angle_1_deg7.995
r_lrange_it7.331
r_lrange_other7.325
r_scangle_it5.404
r_scangle_other5.404
r_mcangle_it5.337
r_mcangle_other5.337
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.386
r_dihedral_angle_3_deg16.886
r_dihedral_angle_4_deg14.877
r_dihedral_angle_1_deg7.995
r_lrange_it7.331
r_lrange_other7.325
r_scangle_it5.404
r_scangle_other5.404
r_mcangle_it5.337
r_mcangle_other5.337
r_mcbond_it3.826
r_mcbond_other3.826
r_scbond_it3.666
r_scbond_other3.666
r_angle_refined_deg1.532
r_angle_other_deg1.332
r_nbd_other0.241
r_nbd_refined0.208
r_symmetry_nbd_other0.202
r_symmetry_nbd_refined0.196
r_xyhbond_nbd_refined0.186
r_nbtor_refined0.171
r_symmetry_xyhbond_nbd_refined0.128
r_symmetry_xyhbond_nbd_other0.125
r_symmetry_nbtor_other0.083
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9538
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing