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Plasmodium vivax aspartyl-tRNA synthetase in complex with L-Asp, Lanthanide, MOPSO and Butanetriol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Morpheous II E1:
0.1 M Buffer System 4 (MOPSO, Bis-Tris) pH 6.5, 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256), 2 mM Lanthanides [0.005M Yttrium(III) chloride hexahydrate, 0.005M Erbium(III) chloride hexahydrate, 0.005M Terbium(III) chloride hexahydrate, 0.005M Ytterbium(III) chloride hexahydrate]
Crystal Properties Matthews coefficient Solvent content 3.05 59.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.737 α = 90 b = 138.737 β = 90 c = 272.751 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 16M 2022-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97627 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.402 128.5 99.5 0.09 0.999 34.1 40.4 60827
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.402 2.444 97.3 0.883 0.935 4.4
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 SAD FREE R-VALUE 2.402 48.628 1.35 60801 3058 99.51 0.1771 0.1753 0.1879 0.21 0.2162
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 5.246 f_angle_d 0.879 f_chiral_restr 0.053 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8061 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement autoPROC data scaling autoPROC data reduction AutoSol phasing PDB_EXTRACT data extraction