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Crystal Structure of Methionine-tRNA ligase / Methionyl-tRNA synthetase (MetRS) from Pseudomonas aeruginosa PAO1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H99 pdb entry 3h99 as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 Anatrace MCSG1 screen, condition D8: 1.5M Ammonium sulfate + BisTris/HCl pH 6.5: PsaeA.10201.a.B1.PW38931 at 23mg/ml + 3mM L-Methionine + 3mM AMP. Tray 320141 d7: cryo: 20% EG + compounds: puck egi5-5
Crystal Properties Matthews coefficient Solvent content 4.75 74.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.9 α = 90 b = 167.9 β = 90 c = 72.24 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 CCD RAYONIX MX-300 Beryllium Lenses 2022-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 50 99.9 0.118 0.129 0.996 13.11 6.261 29094 44.871
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 100 0.62 0.677 0.933 2.88 6.323
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 pdb entry 3h99 as per Morda 2.8 48.47 1.35 29016 1880 99.72 0.1766 0.175 0.1754 0.1999 0.2003 0 51.79
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 13.6496 f_angle_d 0.6526 f_chiral_restr 0.0425 f_plane_restr 0.006 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4073 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 44
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing PHENIX model building Coot model building