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Crystal structure of monooxygenase RutA complexed with 4-Thiouracil.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 100 mM Bis-Tris pH 6.5, 1900 mM ammonium sulphate, 2-5% MPD (v/v),1 mM FMN, 1 mM 4-Thiouracil
Crystal Properties Matthews coefficient Solvent content 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.567 α = 90 b = 87.567 β = 90 c = 95.999 γ = 120
Symmetry Space Group P 31 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 2018-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2 48 100 0.99 22.1 19.8 29258
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 0.953
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 5WAN 2 43.822 29228 1386 99.99 0.205 0.2027 0.2027 0.2454 0.2455 42.855
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] 0.144 0.072 0.144 -0.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_4_deg 19.4 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_1_deg 6.739 r_angle_refined_deg 1.698 r_nbtor_refined 0.317 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.196 r_chiral_restr 0.126 r_xyhbond_nbd_refined 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_4_deg 19.4 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_1_deg 6.739 r_angle_refined_deg 1.698 r_nbtor_refined 0.317 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.196 r_chiral_restr 0.126 r_xyhbond_nbd_refined 0.121 r_symmetry_xyhbond_nbd_refined 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2587 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing