5G0Q

beta-glucuronidase with an activity-based probe (N-alkyl cyclophellitol aziridine) bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VO0PDB ENTRY 3VO0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.68.6
Crystal Properties
Matthews coefficientSolvent content
2.4549.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.512α = 90
b = 44.896β = 114.78
c = 82.216γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS2014-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.6542.699.50.0512.14592632.2
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)
11.651.6899.50.592.24

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 3VO01.6574.6456355290799.40.122890.120460.16922RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.558
r_sphericity_free30.578
r_dihedral_angle_4_deg15.95
r_sphericity_bonded13.36
r_dihedral_angle_3_deg12.676
r_dihedral_angle_1_deg9.191
r_long_range_B_refined4.946
r_long_range_B_other4.944
r_scangle_other4.478
r_scbond_it4.061
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.558
r_sphericity_free30.578
r_dihedral_angle_4_deg15.95
r_sphericity_bonded13.36
r_dihedral_angle_3_deg12.676
r_dihedral_angle_1_deg9.191
r_long_range_B_refined4.946
r_long_range_B_other4.944
r_scangle_other4.478
r_scbond_it4.061
r_scbond_other4.059
r_mcangle_other3.422
r_mcangle_it3.421
r_rigid_bond_restr3.231
r_mcbond_it2.823
r_mcbond_other2.823
r_angle_refined_deg1.859
r_angle_other_deg1.308
r_chiral_restr0.122
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3428
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing