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Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with tetrahydro quinazolinone febrifugine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 10%(w/v) PEG 8K, 20%(v/v) ethylene glycol, 0.03M of each divalent cation and
0.1M MOPS/HEPES-Na
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.644 α = 89.46 b = 90.14 β = 80.34 c = 93.201 γ = 76.07
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 225 mm CCD 2015-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.96725 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 50 98.7 0.078 0.093 0.051 7.6 3.3 80691
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 97.9 0.5 0.604 0.334 0.764 3.2 3958
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 4TWA 2.5 43.76 75422 3988 96.62 0.1876 0.1846 0.1926 0.244 0.2445 RANDOM 37.618
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] -0.77 0.15 -0.1 0.04 -0.15 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.18 r_dihedral_angle_3_deg 16.857 r_dihedral_angle_4_deg 16.771 r_dihedral_angle_1_deg 7.101 r_angle_refined_deg 1.717 r_angle_other_deg 0.844 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.18 r_dihedral_angle_3_deg 16.857 r_dihedral_angle_4_deg 16.771 r_dihedral_angle_1_deg 7.101 r_angle_refined_deg 1.717 r_angle_other_deg 0.844 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15280 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 224
Software Software Software Name Purpose MxCuBE data collection HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data reduction HKL data scaling