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Crystal Structure of Acetyl-coenzyme A synthetase from Leishmania infantum (Ethyl AMP bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SF3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 JCSG+ B4: 10% (w/v) PEG 8000, 8% (v/v) Ethylene glycol, 100 mM Hepes pH 7.5. LeinA.00629.b.B1.PW39174 at 20 mg/mL. Plate 13157 well B4 drop 3. Puck: PSL-1311, Cryo: 20% PEG 200 + 80% crystallant. 2mM ethyl AMP added prior to crystallization.
Crystal Properties Matthews coefficient Solvent content 2.08 40.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.926 α = 90 b = 74.154 β = 90 c = 151.056 γ = 90
Symmetry Space Group P 21 21 21
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 2023-06-08 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 1.55 46.45 100 0.084 0.087 0.024 0.999 16 13.3 96781
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 1.55 1.58 100 1.642 1.706 0.46 0.654 13.6
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 1.55 23.84 1.05 96681 4819 99.98 0.1522 0.1511 0.1602 0.1743 0.183
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 14.064 f_angle_d 0.942 f_chiral_restr 0.059 f_plane_restr 0.01 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5172 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing