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Plasmodium vivax aspartyl-tRNA synthetase in complex with Asp-AMS, Divalent metals, MOPSO and Pentanediol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9M5O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Morpheus II-B3:
0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris)
30% Precipitant Mix 7 (20% w/v PEG 8000, 40% v/v 1,5-
Pentanediol)
2 mM Divalents II (0.005 M Manganese(II) chloride tetrahydrate, 0.005 M Cobalt(II) chloride hexahydrate , 0.005 M Nickel(II) chloride hexahydrate, 0.005M Zinc acetate dihydrate)
Crystal Properties Matthews coefficient Solvent content 3.09 60.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.4 α = 90 b = 139.4 β = 90 c = 273.85 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 2.53 55.23 100 1 10 40.4 53274
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 2.53 2.6 100 0.94 0.3 42.5
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 9M5O 2.53 50.35 1.33 52808 2600 99.28 0.212 0.21 0.212 0.2496 0.2513
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 21.296 f_angle_d 0.571 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7968 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 109
Software Software Software Name Purpose PHENIX refinement xia2 data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction