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Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L-Lysylsulfamoyl Adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BJU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 Human KRS at 35.6 mg/ml, incubated with 5 mM L-Lysylsulfamoyl Adenosine, then mixed 1:1 with Top96(c3): 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M bis-Tris:HCl, pH = 5.5: cryoprotected with 20% ethylene glycol. Tray: 297612c3, puck: KYY0-11
Crystal Properties Matthews coefficient Solvent content 2.5 50.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.87 α = 90 b = 149.87 β = 90 c = 105.23 γ = 120
Symmetry Space Group P 32 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 PILATUS 6M 2018-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.979490 CLSI 08ID-1
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 2.5 49.056 100 0.087 0.093 0.999 16.45 8.677 47408 45.82
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 2.5 2.56 100 0.585 0.621 0.937 3.22 8.91
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 3bju 2.5 49.056 1.35 47385 1980 99.93 0.1592 0.157 0.16 0.2056 0.2091 52.8766
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8017 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 129
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction