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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 6AZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Sitting 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 coefficient Solvent content 2.4 48.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.702 α = 90 b = 87.303 β = 90 c = 341.695 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 CCD ADSC QUANTUM 210 2017-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
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 2.22 47.7 99.9 0.159 0.093 0.99 7.7 7.4 110156
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 2.22 2.26 98.6 0.726 0.434 0.652 2.5 7.1
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 6azn 2.22 42.85 104573 5462 99.94 0.25044 0.24901 0.2523 0.27744 0.2795 RANDOM 32.755
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.712 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 14.12 r_long_range_B_refined 6.077 r_long_range_B_other 6.077 r_dihedral_angle_1_deg 5.005 r_scangle_other 3.421 r_mcangle_it 3.388 r_mcangle_other 3.388 r_mcbond_it 2.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.712 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 14.12 r_long_range_B_refined 6.077 r_long_range_B_other 6.077 r_dihedral_angle_1_deg 5.005 r_scangle_other 3.421 r_mcangle_it 3.388 r_mcangle_other 3.388 r_mcbond_it 2.314 r_mcbond_other 2.313 r_scbond_it 2.294 r_scbond_other 2.293 r_angle_refined_deg 1.433 r_angle_other_deg 1.019 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 13849 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing