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Structural studies of reaction hijacking inhibition of a malaria parasite aspartyl-tRNA synthetase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 15% (w/v) PEG 3000, 20% (v/v) 1,2,4-butanetriol, 1% (w/v) nondetergent sulfobetaine (NDSB) 256, 0.5 mM manganese chloride, 0.5 mM cobalt chloride, and 0.5 mM zinc chloride.
Crystal Properties Matthews coefficient Solvent content 3.11 60.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.045 α = 90 b = 140.045 β = 90 c = 273.02 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 EIGER X 16M 2023-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.36 48.88 99.7 0.1154 0.01836 0.99 24.15 40.5 65749 50.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.38 0.839
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 2.36 48.88 1.34 65749 2000 99.7 0.1884 0.1876 0.1886 0.2146 0.2143 58.16
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 20.883 f_angle_d 0.8494 f_chiral_restr 0.0516 f_bond_d 0.0074 f_plane_restr 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7973 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 76
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing