☰ Navigation Tabs
Crystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Cryptococcus neoformans var. grubii serotype A (H99)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IFI pdb entry 5ifi
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 287 Optimization screen around RigakuReagents Wizard screen 1/2, condition e8: 100mM potassium / sodium phosphate dibasic pH 6.2, 200mM NaCl 13.18% (w/V) PEG 8000: CrneC.00629.a.FS11.PD00460 at 10mg/ml + ethyl-AMP + AcCoA: tray 317932 c7: cryo: 20% EG + compounds: puck: fgi6-9
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.69 α = 90 b = 184.7 β = 93.869 c = 84.84 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 CCD RAYONIX MX-300 Beryllium Lenses 2020-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 50 99.8 0.052 0.06 0.999 15.12 3.78 205272 32.568
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 99.9 0.515 0.605 0.849 2.31 3.627
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE pdb entry 5ifi 1.8 46.94 1.35 205190 2070 99.84 0.164 0.1637 0.1638 0.1898 0.1895 0 37.97
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 12.8185 f_angle_d 0.9141 f_chiral_restr 0.0615 f_plane_restr 0.0095 f_bond_d 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14797 Nucleic Acid Atoms Solvent Atoms 1735 Heterogen Atoms 132
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing PHASER phasing PHENIX model building Coot model building