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[4Fe-4S]-dependent thiouracil desulfidase TudS (DUF523Vcz) soaked with 4-thiouracil (12.65 keV, 7.125 keV (Fe-SAD) and 6.5 keV (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 VAPOR DIFFUSION, HANGING DROP 5.5 293 Anaeroby, 10 mM MgCl2, 0.1 M MES, pH 5.5, 7-9% PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.24 62.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.666 α = 90 b = 85.776 β = 94.1 c = 39.515 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 9M 2020-02-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
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 1.33 39.69 92.2 0.077 0.083 0.998 12.2 6.8 69773
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 1.33 1.5 1.151 1.26 0.548 1.5 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 1.327 39.69 69773 3510 67.6 0.1661 0.1652 0.1657 0.184 0.1853 RANDOM 25.37
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] -0.0621 -0.2322 -0.1758 0.2379
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.15 t_omega_torsion 3.51 t_angle_deg 0.96 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 2236 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 44
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling