8OHU

Crystal structure of Beta-glucuronidase from Acidobacterium capsulatum in complex with glucuronic acid configured isofagamine


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
2.4850.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.046α = 90
b = 44.669β = 97.605
c = 137.173γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979499DiamondI04

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
11.2542.44990.99810.26.2136682
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)
11.251.270.882

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-VALUE1.2542.44136675686698.9420.1650.1640.18414.323
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]
-0.4480.551.049-0.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.183
r_dihedral_angle_4_deg18.799
r_dihedral_angle_3_deg12.64
r_dihedral_angle_1_deg6.291
r_lrange_it5.114
r_lrange_other5.093
r_scangle_it3.985
r_scangle_other3.984
r_scbond_it2.692
r_scbond_other2.691
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.183
r_dihedral_angle_4_deg18.799
r_dihedral_angle_3_deg12.64
r_dihedral_angle_1_deg6.291
r_lrange_it5.114
r_lrange_other5.093
r_scangle_it3.985
r_scangle_other3.984
r_scbond_it2.692
r_scbond_other2.691
r_mcangle_it2.222
r_mcangle_other2.222
r_angle_refined_deg1.931
r_angle_other_deg1.642
r_mcbond_it1.504
r_mcbond_other1.498
r_chiral_restr_other0.431
r_symmetry_nbd_refined0.235
r_nbd_refined0.219
r_symmetry_nbd_other0.187
r_nbtor_refined0.184
r_symmetry_xyhbond_nbd_refined0.183
r_nbd_other0.178
r_xyhbond_nbd_refined0.167
r_chiral_restr0.105
r_symmetry_nbtor_other0.091
r_symmetry_xyhbond_nbd_other0.06
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3453
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing