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Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Asp-AMP, Partially occupied ASP, Mg ion and Butanetriol
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 7.5 293 Morpheus II-G5:
0.1 M Buffer System 5 pH 7.5 (BES, Triethanolamine), 36% Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256), 100 mM Amino acids II (0.2 M DL-Arginine hydrochloride, 0.2 M DL- Threonine, 0.2 M DL-Histidine monohydrochloride monohydrate, 0.2 M DL-5-Hydroxylysine hydrochloride, 0.2 M trans-4-hydroxy-L-proline)
Crystal Properties Matthews coefficient Solvent content 3 59.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.91 α = 90 b = 137.91 β = 90 c = 271.743 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 2022-04-27 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) 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 2.158 119.434 100 0.129 1 19.4 36.2 82470
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 2.158 2.195 99.8 0.363 0.4 17.2
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 2.158 59.717 1.34 81415 3986 98.72 0.1906 0.1892 0.1928 0.2163 0.2174
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 3.109 f_angle_d 0.816 f_chiral_restr 0.048 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8001 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement autoPROC data scaling PHASER phasing PDB_EXTRACT data extraction autoPROC data reduction