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Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with inhibitor 6
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 53.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.6 α = 89.94 b = 90.73 β = 99.37 c = 92.996 γ = 104.31
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 2015-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9797 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 2.17 50 98.1 0.041 0.052 0.031 11 2.7 123090
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 2.17 2.21 93.5 0.479 0.612 0.376 0.703 2.6 5878
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 2.17 40.29 115317 6101 96.56 0.1773 0.1748 0.1771 0.2239 0.2244 RANDOM 33.867
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] -0.65 -0.01 -0.07 0.14 0.01 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.127 r_dihedral_angle_4_deg 16.62 r_dihedral_angle_3_deg 14.546 r_dihedral_angle_1_deg 6.378 r_angle_refined_deg 1.547 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15288 Nucleic Acid Atoms Solvent Atoms 730 Heterogen Atoms 367
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