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Crystal Structure of Acetyl-CoA synthetase from Cryptococcus neoformans H99 in complex with inhibitor HGN-1310 (dd3-027)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8EPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Index F8: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350. CrneC.00629.a.FS11.PD00460 at 10 mg/mL. 2mM HGN-1310 (dd3-027) inhibitor added to the protein prior to crystallization. Plate: 13756 well F8 drop 2. Puck: PSL-1509, Cryo: 20% glycerol + 80% crystallant
Crystal Properties Matthews coefficient Solvent content 2.66 53.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.224 α = 90 b = 176.224 β = 90 c = 159.461 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS EIGER2 XE 9M 2023-11-19 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 2.4 176.22 100 0.177 0.184 0.051 0.998 13 13 98167
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 2.4 2.46 100 1.854 1.927 0.523 0.663 13.5
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 2.4 124.61 1.34 98069 4864 99.99 0.1805 0.1785 0.1824 0.2192 0.218
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 12.541 f_angle_d 0.603 f_chiral_restr 0.046 f_plane_restr 0.006 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14436 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 159
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing