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Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with an isopropyl AMP ester inhibitor
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: 25% PEG 3350, 0.1M HEPES pH 7.5, 0.2M (NH4)2SO4. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM HGN-1195 added to the protein prior to crystallization. plate 13752 well B12 drop 1. Puck: PSL-1803, Cryo: 20% Glycerol + 80% crystallant.
Crystal Properties Matthews coefficient Solvent content 3.36 63.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.487 α = 90 b = 139.487 β = 90 c = 544.117 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 2023-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 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 2.7 49.61 100 0.241 0.248 0.055 0.998 12.3 19.8 87265
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 2.7 2.77 100 2.196 2.252 0.496 0.792 20.4
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 2.7 49.61 1.33 87045 4333 99.92 0.1861 0.1841 0.1864 0.2262 0.2261
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 11.251 f_angle_d 0.632 f_chiral_restr 0.046 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14183 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing