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Structural and biochemical characterization of a non-canonical biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Sitting 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 coefficient Solvent content 2.41 49.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.18 α = 90 b = 86.921 β = 90 c = 342.962 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.75 47.8 100 0.09 0.056 0.998 9 6.5 223984
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) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 0.759 0.546 0.847 1.1 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6azo 1.75 44.48 210888 11028 99.08 0.17539 0.17392 0.1847 0.20354 0.2126 RANDOM 29.138
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] 1.56 1.3 -2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.559 r_dihedral_angle_4_deg 16.864 r_dihedral_angle_3_deg 12.23 r_long_range_B_refined 5.868 r_long_range_B_other 5.868 r_dihedral_angle_1_deg 5.597 r_scangle_other 5.068 r_scbond_it 3.643 r_scbond_other 3.596 r_mcangle_it 3.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.559 r_dihedral_angle_4_deg 16.864 r_dihedral_angle_3_deg 12.23 r_long_range_B_refined 5.868 r_long_range_B_other 5.868 r_dihedral_angle_1_deg 5.597 r_scangle_other 5.068 r_scbond_it 3.643 r_scbond_other 3.596 r_mcangle_it 3.455 r_mcangle_other 3.455 r_mcbond_it 2.84 r_mcbond_other 2.838 r_angle_refined_deg 1.76 r_angle_other_deg 1.069 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 13847 Nucleic Acid Atoms Solvent Atoms 1445 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing