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Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with halofuginone and AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 NafoA.18681.a.B2.PW37988 at 34 mg/ml, incubated with 2 mM MgCl2, AMPPNP, halofuginone, mixed 1:1 with MCSG1(a6): 25% (w/v) PEG-3350, 0.1 M Bis-Tris/HCl, pH = 5.5, 0.2 M ammonium sulfate, cryoprotected with ethlyene glycol. Barcode: 310518a6, puck: xux0-7.
Crystal Properties Matthews coefficient Solvent content 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.29 α = 90 b = 66.54 β = 101.74 c = 112.56 γ = 90
Symmetry Space Group C 1 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 2019-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9785 APS 21-ID-F
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 1.75 50 99.9 0.052 0.06 0.999 15.69 4.173 114792 22.34
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 1.75 1.8 99.9 0.517 0.592 0.813 2.52 4.203
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 6NAB 1.75 42.66 1.35 114783 1918 99.9 0.155 0.154 0.1578 0.18 0.1833 30.61
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 13.097 f_angle_d 0.826 f_chiral_restr 0.054 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7889 Nucleic Acid Atoms Solvent Atoms 888 Heterogen Atoms 206
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction