7PSK

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor GR109


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
2.4750.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.889α = 90
b = 44.573β = 97.599
c = 136.897γ = 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
11.0967.8597.60.9947.93.8201068
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)
11.091.110.803

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-VALUE5g0m1.0942.383200996995697.3420.1730.17190.184911.154
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]
-0.3340.1620.366-0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.827
r_dihedral_angle_1_deg18.657
r_dihedral_angle_4_deg15.322
r_dihedral_angle_3_deg11.525
r_lrange_it4.099
r_lrange_other3.819
r_scangle_it2.86
r_scangle_other2.859
r_angle_refined_deg1.991
r_scbond_it1.948
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.827
r_dihedral_angle_1_deg18.657
r_dihedral_angle_4_deg15.322
r_dihedral_angle_3_deg11.525
r_lrange_it4.099
r_lrange_other3.819
r_scangle_it2.86
r_scangle_other2.859
r_angle_refined_deg1.991
r_scbond_it1.948
r_scbond_other1.948
r_angle_other_deg1.692
r_mcangle_it1.573
r_mcangle_other1.573
r_mcbond_it1.092
r_mcbond_other1.089
r_symmetry_xyhbond_nbd_refined0.281
r_nbd_refined0.265
r_symmetry_nbd_other0.201
r_nbtor_refined0.193
r_nbd_other0.181
r_symmetry_nbd_refined0.138
r_chiral_restr0.115
r_xyhbond_nbd_refined0.114
r_symmetry_nbtor_other0.096
r_symmetry_xyhbond_nbd_other0.033
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3323
Nucleic Acid Atoms
Solvent Atoms566
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing