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Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with Inhibitor 9
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 8.5 293 10%(w/v) PEG 8K, 20%(v/v) ethylene glycol, 0.03M of each ethylene glycol and 0.1M bicine/Trizma base
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.848 α = 89.81 b = 93.158 β = 104.52 c = 91.012 γ = 99.6
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 0.97625 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 0.082 0.094 0.047 8.5 4 82049
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 97.8 0.696 0.81 0.413 0.728 3.8 4050
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4TWA 2.5 40.36 76783 4043 96.99 0.18308 0.18004 0.2397 0.2162 RANDOM 37.173
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] -0.81 0.06 -0.06 0.58 -0.07 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.008 r_dihedral_angle_4_deg 17.125 r_dihedral_angle_3_deg 16.585 r_dihedral_angle_1_deg 6.976 r_angle_refined_deg 1.693 r_angle_other_deg 0.85 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.008 r_dihedral_angle_4_deg 17.125 r_dihedral_angle_3_deg 16.585 r_dihedral_angle_1_deg 6.976 r_angle_refined_deg 1.693 r_angle_other_deg 0.85 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15372 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 220
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