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Crystal structure of the M. abscessus LeuRS editing domain in complex with epetraborole-AMP adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 2 ul of 10 mg/ml protein solution (50 mM Tris pH 7.5, 150 mM NaCl, 2 mM BME) were mixed with 2 ul of crystallization solution (100 mM HEPES pH 7.0, 2.5 M ammonium sulfate)
Crystal Properties Matthews coefficient Solvent content 2.65 53.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.249 α = 90 b = 51.597 β = 90 c = 116.149 γ = 90
Symmetry Space Group P 21 2 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 2020-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.69 50 76.8 0.281 0.095 0.974 4.4 6.8 25482 22.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.72 1.166 0.824 5.5
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 THROUGHOUT 5AGR 2.1 38.57 1.38 14741 1322 96.5 0.1882 0.1841 0.1847 0.2258 0.2266 26.02
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 23.3975 f_angle_d 0.9986 f_chiral_restr 0.0593 f_bond_d 0.0083 f_plane_restr 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1448 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing