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Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with (4-Chlorophenyl)[6-hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl]methanone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B4O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 18.3% (w/v) PEG 3350, 0.1 M Bis-TRIS pH 6.56, 0.133 M lithium acetate
Crystal Properties Matthews coefficient Solvent content 2.33 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.855 α = 90 b = 68.157 β = 90.15 c = 82.807 γ = 90
Symmetry Space Group P 1 21 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 2023-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 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 1.39 19.24 98.9 0.06 0.065 0.024 0.999 14.3 7 152416
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 1.39 1.41 0.405 0.439 0.167 0.948 3.1 6.6
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 1.39 19.14 1.35 152234 7276 98.75 0.1305 0.1292 0.1425 0.156 0.1623 19.446
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 14.113 f_angle_d 0.917 f_chiral_restr 0.075 f_plane_restr 0.012 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4980 Nucleic Acid Atoms Solvent Atoms 741 Heterogen Atoms 136
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement autoPROC data processing PDB_EXTRACT data extraction