☰ Navigation Tabs
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 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 coefficient Solvent content 2.58 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.13 α = 90 b = 122.678 β = 90 c = 135.745 γ = 90
Symmetry Space Group P 2 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 1.59 45.8 100 0.071 0.045 0.999 11.7 6.1 139814
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 1.59 1.62 100 0.726 0.588 0.627 1.6 4.3
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 1.59 45.8 132830 6886 99.95 0.15124 0.15004 0.1632 0.1742 0.1847 RANDOM 22.091
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] -0.28 0.43 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.749 r_dihedral_angle_4_deg 17.31 r_dihedral_angle_3_deg 11.883 r_dihedral_angle_1_deg 6.231 r_long_range_B_refined 5.312 r_long_range_B_other 5.311 r_scangle_other 4.305 r_scbond_it 2.968 r_scbond_other 2.968 r_mcangle_it 2.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.749 r_dihedral_angle_4_deg 17.31 r_dihedral_angle_3_deg 11.883 r_dihedral_angle_1_deg 6.231 r_long_range_B_refined 5.312 r_long_range_B_other 5.311 r_scangle_other 4.305 r_scbond_it 2.968 r_scbond_other 2.968 r_mcangle_it 2.465 r_mcangle_other 2.465 r_angle_refined_deg 1.893 r_mcbond_it 1.809 r_mcbond_other 1.807 r_angle_other_deg 1.144 r_chiral_restr 0.13 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 Atoms Number Protein Atoms 6992 Nucleic Acid Atoms Solvent Atoms 959 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing