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Priestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase 1 complexed with an isoleucyl-adenylate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QU2 Used for main enzyme body (HUP domain, C-terminal domain) phasing experimental model PDB 1WKA Used for editing domain phasing
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 5 mM Ile-AMS and 20 mg/ml wt-HMGH-PmIleRS1 were mixed in 1:1 ratio with the well solution containing: 300 mM lithium sulfate, 150 mM sodium sulfate, and 15 - 25 % PEG3350, 25 mM Hepes-KOH pH=7.5 at 20 oC, 50 mM NaCl. The drop volume of 2 microliters, was equilibrated towards 300 microliters of the well solution at 19 degrees.
Crystal Properties Matthews coefficient Solvent content 3.62 66.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.09 α = 90 b = 127.09 β = 90 c = 163.22 γ = 120
Symmetry Space Group P 31 2 1
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 2020-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000305674358714 SLS X06SA
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 2.9 48.77 92.86 0.06695 0.06867 0.01511 1 30.66 20.8 34322 110.52
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 2.9 3.004 74.11 3.219 3.295 0.7003 0.605 0.98 22
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.9 48.77 0.01 31890 1827 92.9 0.244 0.2424 0.2423 0.2692 0.2687 155.16
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 10.0188 f_angle_d 0.4249 f_chiral_restr 0.0402 f_plane_restr 0.0034 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7401 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building