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Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, Ytterbium, MOPSO and Hexanetriol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9WE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Morpheus II-E2:
0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), recipitant Mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6-Hexanetriol) and 2 mM Lanthanides (0.005 M Yttrium(III) chloride hexahydrate, 0.005 M Erbium(III) chloride hexahydrate, 0.005 M Terbium(III) chloride hexahydrate, 0.005 M Ytterbium(III) chloride hexahydrate)
Crystal Properties Matthews coefficient Solvent content 3.05 59.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.47 α = 90 b = 138.47 β = 90 c = 273.99 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 2023-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.68 61.79 100 1 10.6 40.2 44440
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 2.68 2.73 100 0.3 0.6 42.3
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 FREE R-VALUE 9WE9 2.68 54.93 1.33 44309 2216 99.9 0.21 0.208 0.2086 0.265 0.2619
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 5.162 f_angle_d 0.677 f_chiral_restr 0.044 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8033 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 133
Software Software Software Name Purpose PHENIX refinement xia2 data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction