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Crystal Structure of Acetyl-CoA synthetase in complex with an isopropyl ester AMP inhibitor from Cryptococcus neoformans H99
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 6.2 291 12.5% 8K, 0.2M NaCl, 0.1M K/Na phosphate, CrneC.00629.a.FS11.PD00460 at 10 mg/mL. Plate: Liu-S-058 well D2, HGN1195 cocrystallization (1 mM), Puck: PSL-0704, Cryo: 25% PEG200 + 75% crystallant
Crystal Properties Matthews coefficient Solvent content 2.39 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.879 α = 90 b = 183.779 β = 92.98 c = 84.076 γ = 90
Symmetry Space Group P 1 21 1
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 2022-12-10 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 1.9 183.78 100 0.075 0.081 0.03 0.999 12.9 7.1 170650
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 1.9 1.95 99.9 1.001 1.093 0.435 0.807 6.3
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 1.9 35.89 1.34 170419 8510 99.88 0.175 0.1735 0.1778 0.2037 0.2056
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 12.178 f_angle_d 0.657 f_chiral_restr 0.048 f_plane_restr 0.007 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13767 Nucleic Acid Atoms Solvent Atoms 979 Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing