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Crystal Structure of Acetyl-CoA synthetase in complex with an allyl ester AMP inhibitor from Cryptococcus neoformans H99
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Morpheus F3: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Imidazole/MES, pH 6.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose and 20 mM N-Acetyl-D-Glucosamine, CrneC.00629.a.FS11.PD00460 at 10 mg/mL. SCRI Tray367F3 HGN1194, Puck: PUCK CIDR002 pin5, Cryo: Direct
Crystal Properties Matthews coefficient Solvent content 2.17 43.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.138 α = 66.22 b = 86.889 β = 73.16 c = 105.861 γ = 89.32
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 PILATUS3 S 2M 2022-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0000 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.65 46.03 97 0.068 0.995 7.2 2.2 55144 38.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.73 96.8 0.343 0.872 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 7L4G 2.65 46.03 1.03 55115 2767 97 0.1788 0.1758 0.1803 0.2358 0.2343 47.6307
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14995 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 78
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction