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Crystal structure of monooxygenase RutA complexed with uracil and dioxygen under 1.5 MPa / 15 bars of oxygen pressure.
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, 1mM Uracil
Crystal Properties Matthews coefficient Solvent content 2.67 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.863 α = 90 b = 87.863 β = 90 c = 96.253 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 2018-06-27 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) 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 1.8 48.13 99.5 0.04 23.5 6.3 40105
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 1.8 1.9 0.35
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 1.8 43.97 40074 2076 99.437 0.171 0.1689 0.179 0.212 0.2201 32.804
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] 0.127 0.063 0.127 -0.411
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.312 r_dihedral_angle_3_deg 14.201 r_dihedral_angle_4_deg 14.077 r_lrange_it 7.808 r_lrange_other 7.774 r_dihedral_angle_1_deg 7.109 r_scangle_it 6.608 r_scangle_other 6.599 r_scbond_it 4.6 r_scbond_other 4.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.312 r_dihedral_angle_3_deg 14.201 r_dihedral_angle_4_deg 14.077 r_lrange_it 7.808 r_lrange_other 7.774 r_dihedral_angle_1_deg 7.109 r_scangle_it 6.608 r_scangle_other 6.599 r_scbond_it 4.6 r_scbond_other 4.586 r_mcangle_it 3.534 r_mcangle_other 3.534 r_mcbond_it 2.78 r_mcbond_other 2.778 r_angle_refined_deg 1.883 r_angle_other_deg 1.518 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.186 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.175 r_nbd_other 0.162 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2618 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing