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Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Pyrophosphate, MOPSO and Hexanetriol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9M5M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Morpheus II-C2:
0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), 32.5 Precipitant Mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6-Hexanetriol) and 4 mM Alkalis (0.01 M Rubidium chloride, 0.01 M Strontium acetate, 0.01 M Cesium acetate, 0.01 M Barium acetate)
Crystal Properties Matthews coefficient Solvent content 3.05 59.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.698 α = 90 b = 138.698 β = 90 c = 272.854 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 2022-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.54 29.935 99.8 0.104 0.106 0.016 1 34.1 40.3 51764
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.62 98.6 0.829 0.84 0.13 0.952 40.1
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 9M5M 2.541 29.935 1.34 51670 2538 99.86 0.1685 0.1664 0.1736 0.2089 0.2098
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 5.732 f_angle_d 1.22 f_chiral_restr 0.071 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8002 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 89
Software Software Software Name Purpose PHENIX refinement Aimless data scaling FAST_DP data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction