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[4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) soaked with 4-thiouracil (S-SAD data)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.5 293 Anaeroby, 10 mM MgCl2, 0.1 M MES, pH 5.5, 7-9% PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.27 62.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.165 α = 90 b = 85.519 β = 94.01 c = 39.576 γ = 90
Symmetry Space Group C 1 2 1
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 2019-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.90745 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.759 42.76 91.2 0.081 0.086 0.997 18.9 9.6 39587
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.84 40.4 0.253 0.283 0.955 4.6
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 6Z92 1.759 24.12 39569 1967 88.1 0.1689 0.1679 0.1661 0.1885 0.188 RANDOM 17.67
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] -0.2058 -0.0888 0.3112 -0.1054
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.05 t_omega_torsion 3.33 t_angle_deg 0.91 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_utility_distance t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2226 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 33
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling BUSTER phasing