6AZN

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 13 mg/mL with 150 nL of reservoir: 100 mM citrate buffer at pH 5.5, 12% (w/v) PEG 8000, 20 mM calcium chloride
Crystal Properties
Matthews coefficientSolvent content
2.4149.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.18α = 90
b = 86.921β = 90
c = 342.962γ = 90
Symmetry
Space GroupP 21 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
11.7547.81000.090.0560.99896.5223984
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)
11.751.781000.7590.5460.8471.15.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6azo1.7544.482108881102899.080.175390.173920.20354RANDOM29.138
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]
1.561.3-2.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.559
r_dihedral_angle_4_deg16.864
r_dihedral_angle_3_deg12.23
r_long_range_B_refined5.868
r_long_range_B_other5.868
r_dihedral_angle_1_deg5.597
r_scangle_other5.068
r_scbond_it3.643
r_scbond_other3.596
r_mcangle_it3.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.559
r_dihedral_angle_4_deg16.864
r_dihedral_angle_3_deg12.23
r_long_range_B_refined5.868
r_long_range_B_other5.868
r_dihedral_angle_1_deg5.597
r_scangle_other5.068
r_scbond_it3.643
r_scbond_other3.596
r_mcangle_it3.455
r_mcangle_other3.455
r_mcbond_it2.84
r_mcbond_other2.838
r_angle_refined_deg1.76
r_angle_other_deg1.069
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms13847
Nucleic Acid Atoms
Solvent Atoms1445
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing