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Crystal structure of alanyl-tRNA synthetase L219M mutant in complex with ATP and L-alanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 16% w/v PEG 3,350, 50 mM citric acid, 50 mM bis-tris propane pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.85 56.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.84 α = 90 b = 56.57 β = 102.263 c = 125.63 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 PIXEL DECTRIS EIGER X 9M 2022-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.18 50 99.06 0.996 8.9 6.9 56385 31.830488449
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.24 0.139
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.18006661821 29.89402391 1.3646614981 56377 2818 99.0425494536 0.203080894009 0.201398437604 0.2014 0.234203440402 0.2351 34.2512982481
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 13.1885715251 f_angle_d 1.02116909529 f_chiral_restr 0.0567909240789 f_bond_d 0.00799518698108 f_plane_restr 0.0055574926391
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6652 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 165
Software Software Software Name Purpose PHENIX refinement PHENIX phasing XDS data reduction XDS data scaling