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Crystal Structure of 2-Hydroxyacyl-CoA lyase/synthase TbHACS from Thermoflexaceae bacterium in the Complex with THDP, Formyl-CoA and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 50 mM Calcium Chloride, 0.1 M MES 6.0, 45 % (v/v) PEG 200
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.173 α = 90 b = 182.511 β = 90 c = 123.92 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 16M 2023-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0328 APS 23-ID-B
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 2.2 50 98.7 0.233 0.247 0.081 0.977 6.75 8.2 56818 21.57
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 2.2 2.24 83.7 0.678 0.798 0.404 0.576 1 3
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 2.2 37.38 1.37 56783 2797 98.06 0.1993 0.1975 0.1974 0.2343 0.2342 23.32
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 13.0675 f_angle_d 0.5613 f_chiral_restr 0.0454 f_plane_restr 0.004 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8287 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 245
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MOLREP phasing