☰ Navigation Tabs
Crystal structure of Acetyl-CoA synthetase 2 in complex with AMP from Candida albicans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Berkeley B12: 25% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 200 mM Ammonium sulfate. CaalA.00629.a.FS11.PD00399 at 20 mg/mL. 2mM AMP added to the protein prior to crystallization. Plate: 13581 well B12 drop 1. Puck: PSL-1602, Cryo: 10% PEG 200 + 90% well.
Crystal Properties Matthews coefficient Solvent content 3.36 63.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.463 α = 90 b = 139.463 β = 90 c = 544.987 γ = 120
Symmetry Space Group P 61 2 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 2023-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 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 2.7 49.68 100 0.179 0.183 0.041 0.999 15.3 19.8 87373
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 2.7 2.75 100 2.229 2.29 0.524 0.747 19
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 49.68 1.34 87175 4340 99.95 0.2162 0.215 0.216 0.2397 0.2381
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 12.501 f_angle_d 0.549 f_chiral_restr 0.043 f_plane_restr 0.005 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13960 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 122
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing