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Crystal Structure of Methionyl-tRNA synthetase (MetRS) from Acinetobacter baumannii with bound L-Methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 AcbaB.10201.a.A2.PW37928 at 40 mg/ml incubated with 5 mM L-Met then mixed 1:1 with an equal volume JCSG+(c3): 20% (w/v) PEG-3350, 200 mM ammonium nitrate, cryoprotected with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.91 α = 90 b = 108.41 β = 90.69 c = 78.57 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 CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2016-11-10 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 1.9 37.726 99.3 0.065 0.075 0.998 13.93 3.799 91493 -3 22.22
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 1.9 1.95 98.9 0.45 0.524 0.85 3.11 3.804
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 FREE R-VALUE 1RQG 1.9 37.726 1.35 91459 2061 99.33 0.157 0.1561 0.157 0.1944 0.1954 28.1013
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 12.86 f_angle_d 0.75 f_chiral_restr 0.048 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8603 Nucleic Acid Atoms Solvent Atoms 1012 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction MR-Rosetta phasing