7PSH

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum at 1.24 Angstrom resolution


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
2.4349.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.865α = 90
b = 44.149β = 97.577
c = 136.277γ = 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
11.2474.6997.20.99811.66.1134306
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)
11.261.260.7942.2

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-VALUE5g0m1.2474.69134258682796.8450.170.16860.187816.347
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]
-0.9220.170.6880.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.547
r_dihedral_angle_4_deg17.424
r_dihedral_angle_3_deg12.174
r_dihedral_angle_1_deg6.315
r_lrange_it4.923
r_lrange_other4.85
r_scangle_it3.763
r_scangle_other3.762
r_scbond_it2.563
r_scbond_other2.562
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.547
r_dihedral_angle_4_deg17.424
r_dihedral_angle_3_deg12.174
r_dihedral_angle_1_deg6.315
r_lrange_it4.923
r_lrange_other4.85
r_scangle_it3.763
r_scangle_other3.762
r_scbond_it2.563
r_scbond_other2.562
r_angle_other_deg2.405
r_mcangle_it2.289
r_mcangle_other2.289
r_angle_refined_deg1.959
r_mcbond_it1.6
r_mcbond_other1.6
r_nbd_refined0.232
r_symmetry_nbd_other0.221
r_nbd_other0.217
r_symmetry_xyhbond_nbd_refined0.212
r_nbtor_refined0.191
r_symmetry_nbd_refined0.163
r_symmetry_xyhbond_nbd_other0.121
r_xyhbond_nbd_refined0.12
r_chiral_restr0.103
r_symmetry_nbtor_other0.083
r_bond_other_d0.036
r_gen_planes_other0.02
r_bond_refined_d0.018
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3372
Nucleic Acid Atoms
Solvent Atoms411
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing