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Crystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-butylphosphate 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 5.8 287 Optimization screen around RigakuReagents Wizard screen 1/2, condition e8: 100mM potassium / sodium phosphate dibasic pH 5.8, 200mM NaCl, 12.73% (w/V) PEG 8000: CrneC.00629.a.FS11.PD00460 at 10mg/ml + 1mM TCEP + 1mM butyl-AMP: tray 317934 a7: cryo: 20% EG + compounds: puck: ffb2-5
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.25 α = 90 b = 184.66 β = 93.84 c = 85.13 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 2020-10-01 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 2.25 50 98.4 0.09 0.105 0.995 10.14 3.863 103490 42.752
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 2.25 2.31 97.9 0.547 0.634 0.81 2.6 3.909
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 2.25 40.26 1.36 103450 2160 98.44 0.1764 0.1756 0.1756 0.2128 0.2133 0 53.29
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 13.8637 f_angle_d 0.8231 f_chiral_restr 0.0531 f_plane_restr 0.0088 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13942 Nucleic Acid Atoms Solvent Atoms 819 Heterogen Atoms 139
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing PHENIX model building Coot model building