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Crystal structure of Acetyl-CoA Synthetase in Complex with Adenosine-5'-propylphosphate from Aspergillus fumigatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IFI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 RigakuReagents Morpheus screen, g9:10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02M carboxylic acids (sodium formate, ammonium acetate, trisodium citrate,sodium potassium L-tartrate, sodium oxamate, 0.1M bicine/Trizma base pH8.5; AsfuA.00629.a.FS11.PD00486 at 10 mg/ml, 1mM TCEP, 1mM BSI5663/Propyl-AMP; cryo: direct; tray 313288g9, puck ejj3-5
Crystal Properties Matthews coefficient Solvent content 2.34 47.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.79 α = 68.15 b = 104.21 β = 66.55 c = 125.65 γ = 62.22
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 2019-11-14 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 2.8 50 97.9 0.12 0.139 0.996 10.14 3.9 100485 -3 57.775
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 2.8 2.87 97.5 0.937 1.083 0.703 1.57 4
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 FREE R-VALUE 5IFI 2.8 47.92 1.97 100431 1999 98.06 0.2161 0.2155 0.2161 0.2462 0.2469 65.7636
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 26431 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 156
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing Coot model building