5BK6

Structural and biochemical characterization of a non-canonical biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293Sitting drops were set up with 150 nL protein at 100 mg/mL plus 150 nL reservoir: 100 mM bis-tris chloride buffer at pH 5.5, 17% (w/v) PEG 10000, 100 mM sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.5852.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.13α = 90
b = 122.678β = 90
c = 135.745γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95373Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.5945.81000.0710.0450.99911.76.1139814
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.591.621000.7260.5880.6271.64.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6AZN1.5945.8132830688699.950.151240.150040.1742RANDOM22.091
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]
-0.280.43-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.749
r_dihedral_angle_4_deg17.31
r_dihedral_angle_3_deg11.883
r_dihedral_angle_1_deg6.231
r_long_range_B_refined5.312
r_long_range_B_other5.311
r_scangle_other4.305
r_scbond_it2.968
r_scbond_other2.968
r_mcangle_it2.465
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.749
r_dihedral_angle_4_deg17.31
r_dihedral_angle_3_deg11.883
r_dihedral_angle_1_deg6.231
r_long_range_B_refined5.312
r_long_range_B_other5.311
r_scangle_other4.305
r_scbond_it2.968
r_scbond_other2.968
r_mcangle_it2.465
r_mcangle_other2.465
r_angle_refined_deg1.893
r_mcbond_it1.809
r_mcbond_other1.807
r_angle_other_deg1.144
r_chiral_restr0.13
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6992
Nucleic Acid Atoms
Solvent Atoms959
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing