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Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine and Cladosporin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.1 290 MyulA.00612.a.B1.PW37993 at 28 mg/ml was incubated with 3 mM L-Lysine and cladosporin, then mixed 1:1 with MorpheusCol12opt1 (h7): 0.1 M Tris base/ HCl, pH=9.1, 12.5% (w/v) PEG-1000, 16% (w/v) PEG-3350, 12.5% (v/v) MPD. Tray: 291151h7, puck: wer4-8
Crystal Properties Matthews coefficient Solvent content 3.63 66.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.12 α = 90.05 b = 97.2 β = 104.28 c = 105.83 γ = 117.86
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 2017-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.25 41.316 98.3 0.059 0.069 0.998 12.66 3.885 148550 -3 45.1
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 2.25 2.31 97.5 0.563 0.652 0.804 2.23 3.947
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 5VL1 2.25 41.316 1.98 148513 1954 98.33 0.1536 0.1531 0.1551 0.1949 0.1975 54.3156
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 16.715 f_angle_d 0.845 f_chiral_restr 0.051 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15058 Nucleic Acid Atoms Solvent Atoms 986 Heterogen Atoms 196
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction