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Crystal structure of cytoplasmic Serine-tRNA ligase from Naegleria fowleri in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LSQ PDB entry 3lsq via Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Microlytic MCSG1 screen, B8:25.5% PEG 4000, 15% glycerol, 170mM NaOAc: NafoA.01238.a.B1.PW37973 at 32.5mg/ml + 3mM L-Serine + 3mM AMPPNP + 3mM MgCl2: cryo: direct: tray 286789b8, puck PEM7-1
Crystal Properties Matthews coefficient Solvent content 2.75 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.19 α = 90 b = 168.19 β = 90 c = 111.5 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 CCD RAYONIX MX-300 2016-07-14 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 2.1 42.047 99.8 0.071 0.077 0.999 18.67 7.457 105635 -3 31.28
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 2.1 2.15 100 0.544 0.584 0.897 4.31 7.561
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3lsq via Morda 2.1 42.047 1.36 105584 1960 99.79 0.1588 0.1582 0.161 0.1911 0.1948 0 40.2529
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 10450 Nucleic Acid Atoms Solvent Atoms 1029 Heterogen Atoms 81
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MoRDa phasing Coot model building PHENIX refinement PDB_EXTRACT data extraction