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Priestia megaterium mupirocin-sensitive isoleucyl-tRNA synthetase 1 complexed with mupirocin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 Solution of 20 mg/ml wt-HMGH-PmIleRS1 with added 3 mM mupirocin was mixed in 1:1 ratio with the well solution containing: 400 - 900 mM LiCl and 10 - 20% 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 2.47 50.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.82 α = 90 b = 144.28 β = 95.64 c = 108.37 γ = 90
Symmetry Space Group P 1 21 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 2021-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9999873570222049 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 2.8 60.39 90.26 0.15 0.1767 0.09249 0.993 6.95 3.6 49643 57.17
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 2.8 2.9 75.64 1.288 1.513 0.7865 0.373 0.94 3.6
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 2.8 60.39 0.01 45414 1812 90.27 0.2018 0.1995 0.199 0.258 0.2563 64.61
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 11.7587 f_angle_d 0.4528 f_chiral_restr 0.0396 f_plane_restr 0.0033 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14802 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 91
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building