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Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 during Lugdunomycin Biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.3 M NaCl, 0.1 M Na Cacodylate, pH 6.5, 1.5 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.8 67.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.994 α = 90 b = 185.994 β = 90 c = 75.638 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL DECTRIS PILATUS 2M 2018-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
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 2.08 47.471 99.8 0.399 0.409 0.994 12.5 20.9 87905 33.82
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 2.08 2.13 99 2.839 2.912 0.431 1.7
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 FREE R-VALUE 4osp 2.08 47.471 46574 2313 99.865 0.17 0.1682 0.1775 0.2035 0.2073 28.094
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] -0.006 -0.003 -0.006 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.784 r_dihedral_angle_4_deg 20.911 r_dihedral_angle_3_deg 13.182 r_lrange_it 7.876 r_lrange_other 7.778 r_dihedral_angle_1_deg 6.304 r_scangle_it 4.324 r_scangle_other 4.187 r_scbond_it 2.808 r_mcangle_it 2.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.784 r_dihedral_angle_4_deg 20.911 r_dihedral_angle_3_deg 13.182 r_lrange_it 7.876 r_lrange_other 7.778 r_dihedral_angle_1_deg 6.304 r_scangle_it 4.324 r_scangle_other 4.187 r_scbond_it 2.808 r_mcangle_it 2.768 r_mcangle_other 2.762 r_scbond_other 2.676 r_angle_refined_deg 1.83 r_mcbond_it 1.751 r_mcbond_other 1.741 r_angle_other_deg 1.518 r_nbd_other 0.238 r_nbd_refined 0.208 r_symmetry_nbd_refined 0.201 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.144 r_chiral_restr 0.094 r_ncsr_local_group_1 0.094 r_symmetry_xyhbond_nbd_other 0.093 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3500 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing