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Priestia megaterium mupirocin-resistant isoleucyl-tRNA synthetase 2 complexed with mupirocin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JZQ Used as a search model for initial phase determination. experimental model PDB 1JZS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1-0.4 M Potassium tartrate
15-25 % (w/v) PEG3350
12.5 mM Hepes-KOH pH=7,5 at 20 oC
25 mM NaCl
5 mM lithium-mupirocin
8.25 mg/ml wt-HVGH-BmIleRS2
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.58 α = 90 b = 124.83 β = 90 c = 114.46 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 2M 2.9 T superbend magnet 2020-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9999951402559115 SLS X06DA
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 1.901 48.23 90.6 0.13 0.1352 0.03685 0.999 14.93 13.3 101302 30.49
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 1.901 1.969 74.27 2.579 2.681 0.7203 0.452 1.01 13.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1JZS 1.901 48.23 0.01 81179 4034 93.02 0.1846 0.1826 0.1872 0.2224 0.2266 Random selection 40.53
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 14.2132 f_angle_d 0.9094 f_chiral_restr 0.2127 f_bond_d 0.0084 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8173 Nucleic Acid Atoms Solvent Atoms 764 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building