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Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl](3-hydroxyphenyl)methanone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EX9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 15% (w/v) PEG monomethyl ether, 0.1 M MES pH 6.14, 0.122 M ammonium acetate, 5% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.995 α = 90 b = 69.369 β = 93.64 c = 69.182 γ = 90
Symmetry Space Group C 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 100 PIXEL DECTRIS EIGER2 X 16M 2022-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.38 53.18 99.1 0.047 0.051 0.019 0.999 16.5 6.9 79713
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 1.38 1.4 0.686 0.741 0.278 0.897 2.1 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.38 42.99 1.36 79659 3961 98.99 0.1386 0.1373 0.1386 0.1641 0.1652 25.879
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.623 f_angle_d 1.172 f_chiral_restr 0.085 f_plane_restr 0.011 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2548 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 100
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement autoPROC data processing PDB_EXTRACT data extraction