6AZQ

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 200 nL protein at 13 mg/mL plus 200 nL reservoir: 11.9% (w/v) PEG 8000, 27 mM calcium chloride, 100 mM citrate buffer at pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.448.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.702α = 90
b = 87.303β = 90
c = 341.695γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102017-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95370Australian SynchrotronMX1

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
12.2247.799.90.1590.0930.997.77.4110156
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)
12.222.2698.60.7260.4340.6522.57.1

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 REPLACEMENTTHROUGHOUT6azn2.2242.85104573546299.940.250440.249010.27744RANDOM32.755
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]
1.45-1.07-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.712
r_dihedral_angle_4_deg18.125
r_dihedral_angle_3_deg14.12
r_long_range_B_refined6.077
r_long_range_B_other6.077
r_dihedral_angle_1_deg5.005
r_scangle_other3.421
r_mcangle_it3.388
r_mcangle_other3.388
r_mcbond_it2.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.712
r_dihedral_angle_4_deg18.125
r_dihedral_angle_3_deg14.12
r_long_range_B_refined6.077
r_long_range_B_other6.077
r_dihedral_angle_1_deg5.005
r_scangle_other3.421
r_mcangle_it3.388
r_mcangle_other3.388
r_mcbond_it2.314
r_mcbond_other2.313
r_scbond_it2.294
r_scbond_other2.293
r_angle_refined_deg1.433
r_angle_other_deg1.019
r_chiral_restr0.094
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms13849
Nucleic Acid Atoms
Solvent Atoms409
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing