8OHT

Crystal structure of Beta-glucuronidase from Acidobacterium capsulatum in complex with competitive inhibitor derrived from siastatin B


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.5 M AmSO4 1 M LiSO4 0.1 M Trisodium Citrate
Crystal Properties
Matthews coefficientSolvent content
2.5451.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.75α = 90
b = 44.67β = 97.461
c = 136.268γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-12-19MSINGLE 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
11.0567.6596.50.99915.16.3221410
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)
11.051.070.5821.4

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-VALUE1.0567.6482214091101196.2990.1670.16690.177413.041
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]
-0.2730.2270.505-0.282
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.268
r_dihedral_angle_4_deg14.875
r_dihedral_angle_3_deg12.569
r_dihedral_angle_1_deg6.203
r_lrange_it4.4
r_lrange_other4.166
r_scangle_it3.141
r_scangle_other3.118
r_scbond_it2.263
r_scbond_other2.224
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.268
r_dihedral_angle_4_deg14.875
r_dihedral_angle_3_deg12.569
r_dihedral_angle_1_deg6.203
r_lrange_it4.4
r_lrange_other4.166
r_scangle_it3.141
r_scangle_other3.118
r_scbond_it2.263
r_scbond_other2.224
r_angle_refined_deg2.049
r_angle_other_deg1.703
r_mcangle_it1.658
r_mcangle_other1.658
r_mcbond_it1.151
r_mcbond_other1.151
r_nbd_refined0.251
r_symmetry_xyhbond_nbd_refined0.229
r_xyhbond_nbd_refined0.214
r_nbd_other0.208
r_symmetry_nbd_other0.198
r_nbtor_refined0.193
r_symmetry_nbd_refined0.173
r_symmetry_xyhbond_nbd_other0.137
r_chiral_restr0.121
r_chiral_restr_other0.111
r_symmetry_nbtor_other0.092
r_bond_refined_d0.02
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 Atoms3470
Nucleic Acid Atoms
Solvent Atoms584
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing