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Crystal structure of lysyl-tRNA synthetase LysRS from Burkholderia thailandensis bound to lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BBU pdb entry 1bbu
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 ButhA.00612.a.A1 PS01208 at 18.9 mg/mL against Morpheus H5, 10% PEG 20,000, 20% PEG 550 MME, 0.1 M MOPS/Hepes, 20 mM glutamate, 20 mM alanine, 20 mM glycine, 20 mM serine, 20 mM lysine, crystal tracking ID 232983h5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.73 66.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.22 α = 90 b = 118.54 β = 113.23 c = 94.54 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 RIGAKU SATURN 944+ 2012-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 50 98.1 0.08 10.87 2.8 68404 67117 -3 39.185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 96.1 0.468 2.27
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT pdb entry 1bbu 2.4 50 67095 3401 98.27 0.1909 0.1892 0.1902 0.2228 0.2238 RANDOM 32.9777
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] 0.31 0.86 -1.21 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.826 r_dihedral_angle_4_deg 17.592 r_dihedral_angle_3_deg 14.361 r_dihedral_angle_1_deg 6.003 r_angle_refined_deg 1.444 r_angle_other_deg 1.103 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.826 r_dihedral_angle_4_deg 17.592 r_dihedral_angle_3_deg 14.361 r_dihedral_angle_1_deg 6.003 r_angle_refined_deg 1.444 r_angle_other_deg 1.103 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7588 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 20
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction