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The structure of a CoA-dependent acyl-homoserine lactone synthase, RpaI, with the adduct of SAH and p-coumaroyl CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W8E PDB entry 5W8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 282 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.519 α = 90 b = 100.512 β = 90 c = 105.047 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD MARMOSAIC 300 mm CCD 2018-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.85 50 97.4 0.114 0.124 0.047 5.9 6.2 38339
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 96.1 0.765 0.837 0.326 0.701 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 PDB entry 5W8E 1.85 25 35779 1880 95.88 0.1887 0.1866 0.1869 0.2288 0.2291 RANDOM 21.701
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] -0.33 -0.19 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.036 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 14.507 r_dihedral_angle_1_deg 5.505 r_angle_refined_deg 1.491 r_chiral_restr 0.099 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3389 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 170
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction BUCCANEER phasing