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Crystal structure of Aspartyl-tRNA synthetase from Mycobacterium tuberculosis complexed with L-Aspartic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 MytuD.00145.b.M1.PD00305 at 10.3 mg/ml was incubated with 1 mM L-aspartic acid, then mixed 1:1 with Morpheus (h1): 10% (w/v) PEG-20000, 20% (v/v) PEG MME 550, 0.1 M MES/imidazole, pH = 6.5, 0.02 M each L-glutamate, DL-alanine, glycine, DL-lysine, DL-serine, Tray 251523h1, puck gdy9-5
Crystal Properties Matthews coefficient Solvent content 2.88 57.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.72 α = 90 b = 158.24 β = 93.77 c = 75.74 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 ADSC QUANTUM 315r 2017-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0000 ALS 8.2.2
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 2.65 43.254 99.8 0.049 0.056 0.999 16.48 4.143 44023 -3 62.64
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 2.65 2.72 99.7 0.517 0.592 0.948 2.59 4.253
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 4RMF 2.65 43.254 1.35 43910 1973 99.56 0.2257 0.2247 0.2303 0.245 0.2494 102.3951
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 14.478 f_angle_d 0.46 f_chiral_restr 0.057 f_plane_restr 0.005 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8225 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 50
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MoRDa phasing