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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 291.15 20% PEG 3350, 0.1 M Na Malonate, 0.1 M BIS-TRIS prop, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.828 α = 90 b = 59.965 β = 102.513 c = 88.428 γ = 90
Symmetry Space Group I 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 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) R Sym 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 1.08 49.3 95.4 0.054 0.054 0.064 0.999 13.4 3.1 428985 12.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.08 1.108 99.1 0.679 0.679 0.827 0.648 2.1 3
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 1.08 49.298 191427 9588 99.91 0.147 0.1457 0.147 0.1653 0.1658 11.858
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] -0.316 -0.244 0.492 -0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.615 r_dihedral_angle_4_deg 20.115 r_dihedral_angle_3_deg 10.422 r_dihedral_angle_1_deg 6.158 r_lrange_it 4.235 r_lrange_other 4.057 r_scangle_it 3.056 r_scangle_other 3.056 r_angle_refined_deg 2.215 r_scbond_it 2.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.615 r_dihedral_angle_4_deg 20.115 r_dihedral_angle_3_deg 10.422 r_dihedral_angle_1_deg 6.158 r_lrange_it 4.235 r_lrange_other 4.057 r_scangle_it 3.056 r_scangle_other 3.056 r_angle_refined_deg 2.215 r_scbond_it 2.117 r_scbond_other 2.117 r_mcangle_it 1.658 r_angle_other_deg 1.654 r_mcangle_other 1.651 r_mcbond_it 1.114 r_mcbond_other 1.101 r_symmetry_xyhbond_nbd_other 0.318 r_nbd_other 0.285 r_symmetry_nbd_refined 0.269 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.225 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.171 r_chiral_restr 0.127 r_symmetry_nbtor_other 0.089 r_ncsr_local_group_1 0.077 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3730 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing