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Human asparaginyl-tRNA synthetase bound to adenosine 5'-sulfamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20% (v/v) glycerol, 40 mM potassium phosphate and 14% polyethylene glycol 8,000, and 100-mM Tris pH 7.6
Crystal Properties Matthews coefficient Solvent content 2.33 47.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.851 α = 90 b = 126.285 β = 90 c = 160.598 γ = 90
Symmetry Space Group P 21 21 21
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 2022-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.9 49.29 99.9 0.163 0.192 0.072 0.998 7.5 6.9 185028 27.52
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 1.9 1.93 2.601 3.07 1.186 0.502
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 5XIX 1.9 49.29 1.34 184540 9326 99.68 0.1827 0.1809 0.1819 0.2172 0.2174 37.02
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 12.8631 f_angle_d 0.8601 f_chiral_restr 0.051 f_plane_restr 0.0086 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14007 Nucleic Acid Atoms Solvent Atoms 1589 Heterogen Atoms 224
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing