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Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with a propyne AMP ester inhibitor and CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Berkeley B12: 200 mM Ammonium sulfate, 25% (w/v) PEG 3350, 100 mM HEPES pH 7.5. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1196 and 2mM CoA added to the protein prior to crystallization. plate 13753 well B12 drop 2. Puck: PSL-1314, Cryo: 20% PEG 200 + 80% crystallant.
Crystal Properties Matthews coefficient Solvent content 3.34 63.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.179 α = 90 b = 139.179 β = 90 c = 543.69 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS EIGER2 XE 9M 2023-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9785 NSLS-II 19-ID
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 2.75 48.62 100 0.18 0.185 0.041 0.999 15.2 20 82254
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 2.75 2.82 100 2.487 2.547 0.55 0.823 21.1
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 2.75 48.62 1.33 82003 4105 99.87 0.2043 0.2025 0.2068 0.2394 0.2398
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 11.326 f_angle_d 0.813 f_chiral_restr 0.05 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14375 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 283
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing