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Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with a cyclopentyl ester AMP 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-1192 added to the protein prior to crystallization. Plate: plate 13750 well B12, drop 2. Puck: PSL-1715, Cryo: 20% Glycerol + 80% crystallant.
Crystal Properties Matthews coefficient Solvent content 3.35 63.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.409 α = 90 b = 139.409 β = 90 c = 543.793 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 2.35 49.58 100 0.207 0.212 0.047 0.998 12.6 19.9 130936
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 2.35 2.41 100 2.253 2.31 0.508 0.786 20.6
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 FREE R-VALUE 2.35 49.58 1.33 130716 6633 99.97 0.1823 0.1809 0.1845 0.2096 0.2129
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 12.463 f_angle_d 0.705 f_chiral_restr 0.049 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14257 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 123
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing