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Crystal Structure of Acetyl-CoA synthetase in complex with a propyne 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 A7, HGN1196 cocrystallization (1 mM), Puck: PSL-0704, Cryo: 25% PEG200 + 75% crystallant
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.079 α = 70.11 b = 81.827 β = 74.37 c = 101.32 γ = 88.37
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 91.56 97.3 0.057 0.067 0.035 0.999 11.1 3.6 158139
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 96.2 0.688 0.832 0.458 0.752 3.3
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 24.67 1.96 158000 7840 97.24 0.1745 0.1731 0.1722 0.2006 0.1998
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 12.127 f_angle_d 0.827 f_chiral_restr 0.057 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15395 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 95
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing