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Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AZO PDB entry 6AZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 1 uL 20 mg/mL protein + 1 uL 24% PEG6000, 0.1 M Bis-Tris propane
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.95 α = 118.403 b = 76.55 β = 89.606 c = 93.59 γ = 103.065
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 2018-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
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 2.1 81.57 90.4 0.068 9.16 2.13 91216
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 2.1 2.2 92.2 0.176 4.76 2.16
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 6AZO 2.1 70.57 91215 4561 90.669 0.181 0.1785 0.1884 0.2283 0.2355 20.286
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] 1.444 0.129 -2.53 -0.294 -0.795 0.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.83 r_dihedral_angle_other_3_deg 28.14 r_dihedral_angle_4_deg 18.848 r_dihedral_angle_3_deg 14.997 r_dihedral_angle_1_deg 7.014 r_lrange_it 4.519 r_lrange_other 4.428 r_scangle_it 3.191 r_scangle_other 3.19 r_mcangle_it 2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.83 r_dihedral_angle_other_3_deg 28.14 r_dihedral_angle_4_deg 18.848 r_dihedral_angle_3_deg 14.997 r_dihedral_angle_1_deg 7.014 r_lrange_it 4.519 r_lrange_other 4.428 r_scangle_it 3.191 r_scangle_other 3.19 r_mcangle_it 2.25 r_mcangle_other 2.25 r_scbond_it 2.033 r_scbond_other 2.033 r_angle_refined_deg 1.561 r_mcbond_it 1.478 r_mcbond_other 1.478 r_angle_other_deg 1.292 r_symmetry_xyhbond_nbd_refined 0.216 r_nbd_refined 0.196 r_nbd_other 0.196 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.152 r_symmetry_nbd_refined 0.143 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13411 Nucleic Acid Atoms Solvent Atoms 783 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data scaling Coot model building MOLREP phasing XDS data reduction