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Plasmodium vivax aspartyl-tRNA synthetase in complex with AMS, Mg ion, Iodides and Pentaethylene glycol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Morpheus B5:
0.1 M Buffer System 2 pH 7.5 (Sodium HEPES and MOPS), 30% Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000) and 0.09 M Halogens (0.3 M Sodium fluoride; 0.3 M Sodium bromide; 0.3 M Sodium iodide)
Crystal Properties Matthews coefficient Solvent content 3.07 59.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.685 α = 90 b = 138.685 β = 90 c = 274.992 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 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 2.228 120.105 100 0.196 0.997 16.2 37.6 76798
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 2.228 2.267 100 0.261 0.5 20.9
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 2.228 45.832 1.33 76368 3854 99.46 0.1911 0.1895 0.196 0.2208 0.2249
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 5.562 f_angle_d 0.704 f_chiral_restr 0.047 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8132 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement autoPROC data scaling autoPROC data reduction PHASER phasing PDB_EXTRACT data extraction