☰ Navigation Tabs
Plasmodium vivax aspartyl-tRNA synthetase in complex with AMP, Divalent metals, MOPSO 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 6.5 293 Morpheus II-B1:
0.1 M Buffer System 4 pH 6.5 (MOPSO, Bis-Tris), 35% Precipitant Mix 5 (0% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256) 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, 0.005 M Zinc acetate dihydrate)
Crystal Properties Matthews coefficient Solvent content 3.07 59.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.032 α = 90 b = 139.032 β = 90 c = 273.339 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 2.391 120.405 99.8 0.262 0.999 13.2 40.7 62198
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 2.391 2.432 98.1 0.413 38.8
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 2.391 110.188 1.33 61528 3049 98.71 0.1936 0.192 0.2059 0.2244 0.2361
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 5.238 f_angle_d 0.78 f_chiral_restr 0.048 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8097 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 101
Software Software Software Name Purpose PHENIX refinement autoPROC data scaling PHASER phasing PDB_EXTRACT data extraction autoPROC data reduction