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Crystal structure of Acetyl-CoA synthetase 2 in complex with Adenosine-5'-propylphosphate from Candida albicans
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 7.5 287 Microlytics MCSG1 screen, condition G10: 100mM Mg-formate, 15% (wV) PEG 3350: CaalA.00629.a.FS11.PD00399 at 10mg/ml + 1mM Propyl-AMP + 1mM TCEP: tray: 313278g10: cryo: 25% EG + compounds: puck cfh0-10
Crystal Properties Matthews coefficient Solvent content 2.56 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.92 α = 90 b = 166.92 β = 90 c = 166.92 γ = 90
Symmetry Space Group P 41 3 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 PILATUS3 6M DCM, Si-111 2020-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 2.9 50 99.9 0.081 0.082 1 34.52 38.471 18239 104.656
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 2.9 2.98 100 2.617 2.655 0.634 1.55 35.162
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 THROUGHOUT pdb entry 5ifi 2.9 48.19 1.34 18188 1881 99.98 0.2355 0.2319 0.2306 0.2666 0.2665 118.4022
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 11.83 f_angle_d 0.493 f_chiral_restr 0.042 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4801 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 27
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing