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Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound with triuret
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 8 291 1 uL 20 mg/mL protein + 1 uL 24% w/v PEG6000, 0.1 M Bis-Tris propane, 1 mM triuret, pH 8
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.53 α = 90 b = 114.44 β = 90 c = 142.93 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 PILATUS 6M 2018-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033320 APS 23-ID-D
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 1.45 60.62 100 0.051 20.99 7.47 150183
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 1.45 1.55 100 0.547 3.97 7.21
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 1.45 60.616 150183 7510 99.957 0.173 0.172 0.1724 0.1898 0.1901 19.158
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] -0.08 -0.549 0.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.706 r_dihedral_angle_4_deg 17.324 r_dihedral_angle_3_deg 12.733 r_dihedral_angle_1_deg 6.367 r_lrange_it 5.318 r_lrange_other 5.318 r_scangle_it 4.546 r_scangle_other 4.546 r_scbond_it 3.083 r_scbond_other 3.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.706 r_dihedral_angle_4_deg 17.324 r_dihedral_angle_3_deg 12.733 r_dihedral_angle_1_deg 6.367 r_lrange_it 5.318 r_lrange_other 5.318 r_scangle_it 4.546 r_scangle_other 4.546 r_scbond_it 3.083 r_scbond_other 3.083 r_mcangle_other 2.359 r_mcangle_it 2.356 r_angle_refined_deg 1.873 r_mcbond_it 1.703 r_mcbond_other 1.696 r_angle_other_deg 1.594 r_nbd_other 0.225 r_nbd_refined 0.219 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.142 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.101 r_ncsr_local_group_3 0.1 r_ncsr_local_group_6 0.093 r_ncsr_local_group_4 0.087 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_5 0.084 r_ncsr_local_group_1 0.081 r_ncsr_local_group_2 0.079 r_gen_planes_refined 0.02 r_bond_refined_d 0.013 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6698 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing Coot model building