7PSJ

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VL166


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
2.4549.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.393α = 90
b = 44.117β = 97.579
c = 136.708γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-01-18MSINGLE 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
11.5575.1199.90.9977.13.971878
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)
11.551.580.793

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-VALUE5g0m1.5575.11271856359399.7960.1960.19460.222721.816
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]
-1.5350.6843.605-2.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.61
r_dihedral_angle_4_deg16.476
r_dihedral_angle_3_deg13.328
r_dihedral_angle_1_deg6.689
r_lrange_it5.329
r_lrange_other5.236
r_scangle_it3.799
r_scangle_other3.798
r_mcangle_other2.576
r_mcangle_it2.574
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.61
r_dihedral_angle_4_deg16.476
r_dihedral_angle_3_deg13.328
r_dihedral_angle_1_deg6.689
r_lrange_it5.329
r_lrange_other5.236
r_scangle_it3.799
r_scangle_other3.798
r_mcangle_other2.576
r_mcangle_it2.574
r_angle_other_deg2.527
r_scbond_it2.497
r_scbond_other2.497
r_mcbond_it1.752
r_mcbond_other1.729
r_angle_refined_deg1.643
r_symmetry_nbd_other0.213
r_symmetry_xyhbond_nbd_refined0.209
r_nbd_refined0.206
r_chiral_restr0.2
r_nbd_other0.198
r_symmetry_nbd_refined0.191
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.15
r_symmetry_nbtor_other0.08
r_bond_other_d0.036
r_gen_planes_other0.014
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_symmetry_xyhbond_nbd_other0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3312
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing