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Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound with biuret
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XIX PDB entry 6XIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 291 1uL 10 mg/mL TrtA + 1 uL 26% w/v PEG6000, 0.1 M Bis-Tris propane, 30 mM biuret, pH 9
Crystal Properties Matthews coefficient Solvent content 2.15 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.63 α = 90 b = 114.18 β = 90 c = 141.47 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 2019-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.992 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.78 57.09 99.8 0.062 12.44 3.85 80968
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.88 99.9 0.369 4.26 3.77
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 6XIX 1.78 57.09 80968 4049 99.928 0.157 0.1557 0.1681 0.1872 0.1976 27.334
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] -1.077 -1.102 2.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.407 r_dihedral_angle_4_deg 18.523 r_dihedral_angle_3_deg 12.863 r_dihedral_angle_1_deg 6.519 r_lrange_it 6.51 r_lrange_other 6.407 r_scangle_it 5.693 r_scangle_other 5.693 r_scbond_it 3.85 r_scbond_other 3.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.407 r_dihedral_angle_4_deg 18.523 r_dihedral_angle_3_deg 12.863 r_dihedral_angle_1_deg 6.519 r_lrange_it 6.51 r_lrange_other 6.407 r_scangle_it 5.693 r_scangle_other 5.693 r_scbond_it 3.85 r_scbond_other 3.85 r_mcangle_it 2.968 r_mcangle_other 2.968 r_mcbond_it 2.277 r_mcbond_other 2.259 r_angle_refined_deg 1.703 r_angle_other_deg 1.468 r_symmetry_xyhbond_nbd_refined 0.235 r_nbd_refined 0.21 r_nbd_other 0.204 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.155 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.083 r_gen_planes_other 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6698 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data scaling MOLREP phasing XDS data reduction