7PSI

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor ME727


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G0M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.5 M AmSO4 1 M LiSO4 0.1 M Trisodium Citrate
Crystal Properties
Matthews coefficientSolvent content
2.4549.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.656α = 90
b = 44.469β = 97.61
c = 136.714γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.911880DiamondI04-1

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
11.2574.6298.40.9936.63.7133814
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)
11.251.270.68

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-VALUE5g0m1.2574.6133776661798.070.1690.16850.184113.788
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]
-0.5850.520.449-0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.432
r_dihedral_angle_4_deg15.297
r_dihedral_angle_3_deg12.201
r_dihedral_angle_1_deg6.262
r_lrange_it4.527
r_lrange_other4.302
r_scangle_it3.34
r_scangle_other3.329
r_angle_other_deg2.388
r_scbond_it2.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.432
r_dihedral_angle_4_deg15.297
r_dihedral_angle_3_deg12.201
r_dihedral_angle_1_deg6.262
r_lrange_it4.527
r_lrange_other4.302
r_scangle_it3.34
r_scangle_other3.329
r_angle_other_deg2.388
r_scbond_it2.298
r_scbond_other2.203
r_mcangle_it1.942
r_mcangle_other1.942
r_angle_refined_deg1.803
r_mcbond_it1.301
r_mcbond_other1.28
r_nbd_refined0.212
r_symmetry_nbd_other0.21
r_symmetry_xyhbond_nbd_refined0.2
r_nbd_other0.197
r_nbtor_refined0.188
r_xyhbond_nbd_refined0.133
r_symmetry_nbd_refined0.111
r_chiral_restr0.098
r_symmetry_nbtor_other0.088
r_symmetry_xyhbond_nbd_other0.081
r_bond_other_d0.036
r_gen_planes_other0.02
r_bond_refined_d0.016
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3458
Nucleic Acid Atoms
Solvent Atoms466
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing