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Crystal structure of polyketoacyl-CoA thiolase from Burkholderia sp. in complex with acetyl-coA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9BWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M lithium sulfate, 0.1 M sodium chloride, 0.1 M Bis-Tris ph 6.5, 20 % PEG 3,350 and 10 % hexanediol
Crystal Properties Matthews coefficient Solvent content 3.12 60.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.292 α = 90 b = 130.292 β = 90 c = 121.802 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2023-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0000 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.23 44.49 99.9 0.155 0.992 15.1 13.1 51555 49.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.31 0.309
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 FREE R-VALUE 2.23 44.49 1.34 51555 1986 99.95 0.1925 0.1913 0.1917 0.2217 0.2225 64.57
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 7.7344 f_angle_d 0.6293 f_chiral_restr 0.0448 f_plane_restr 0.0045 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5724 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing