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Priestia megaterium inactive HIGH motif mutant of type1 isoleucyl-tRNA synthetase complexed with an isoleucyl-adenylate analogue.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C9E experimental model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 5 mM Ile-AMS and 20 mg/ml mut-GMHH-PmIleRS1 were mixed in 1:1 ratio with the well solution containing: 300 mM lithium sulfate, 150 mM sodium sulfate, and 15 - 25 % PEG3350, 25 mM Hepes-KOH pH=7.5 at 20 oC, 50 mM NaCl. The drop volume of 2 microliters, was equilibrated towards 300 microliters of the well solution at 4 degrees.
Crystal Properties Matthews coefficient Solvent content 3.62 66.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.04 α = 90 b = 127.04 β = 90 c = 163.38 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 PIXEL DECTRIS EIGER X 16M 2020-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000305674358714 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.1 48.81 90.83 0.1224 0.1255 0.02748 0.999 19.7 20.7 28199 110.31
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 3.1 3.211 90.83 3.731 3.82 0.8137 0.586 1 21.8
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 3.1 48.81 0.01 25630 1830 90.87 0.2418 0.2391 0.2392 0.2763 0.2766 153.23
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 11.9098 f_angle_d 0.4298 f_chiral_restr 0.0403 f_plane_restr 0.0034 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7401 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building