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Crystal Structure of Acetyl-CoA synthetase in complex with a cyclopentyl ester AMP inhibitor from Cryptococcus neoformans H99 (tetragonal form)
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 Morpheus G5 (75% dilution): 15%(v/v) PEG 500 MME, 7.5%(w/v) PEG 20000, 75 mM HEPES/MOPS, pH 7.5, 15 mM Sodium formate, 15 mM Ammonium acetate, 15 mM Sodium citrate tribasic, 15 mM Potassium sodium tartrate and 15 mM Sodium oxamate, CrneC.00629.a.FS11.PD00460 at 10 mg/mL. Plate: Liu-S-057, well E3 , HGN1192 soak for 24 hours (1 mM), Puck: PSL-0712, Cryo Morpheus G5 (100%): 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM HEPES/MOPS, pH 7.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM Potassium sodium tartrate and 20 mM Sodium oxamate
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.16 α = 90 b = 174.16 β = 90 c = 158.927 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 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 2.9 174.16 100 0.166 0.17 0.037 0.999 15.9 20.7 54700
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 2.9 2.98 100 2.312 2.365 0.498 0.796 22.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 25.34 1.34 54475 2610 99.91 0.1919 0.1903 0.2226 0.204
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 12.21 f_angle_d 0.678 f_chiral_restr 0.05 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14086 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 87
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing