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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 7.5 mg/ml protein solution (50 mM Tris pH 7.5, 150 mM NaCl. 2 mM BME) was mixed with crystallization solution (100 mM HEPES, pH 7.5, 2% PEG400, 2.1 M ammonium sulfate, 10 mM AMP, 1 mM epetraborole, 15% glycerol)
Crystal Properties Matthews coefficient Solvent content 2.3 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.439 α = 90 b = 37.107 β = 112.279 c = 100.287 γ = 90
Symmetry Space Group C 1 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 PILATUS3 6M 2021-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.52131 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.52 92.97 94.21 0.1 0.11 0.044 7.7 5.5 56594 17.5
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 1.71 1.75 99.57 0.457 0.506 0.214 0.833 1.4 5.35
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 THROUGHOUT 5AGR 1.7 92.8 1.41 56594 4142 99.38 0.1861 0.184 0.1864 0.2267 0.2268 Random selection 21.84
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 21.3447 f_angle_d 1.2161 f_chiral_restr 0.0686 f_bond_d 0.0128 f_plane_restr 0.0088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2845 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing