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Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with Halofuginone
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 6.5 293 10%(w/v) PEG 4K, 20%(v/v) glycerol, 0.03M of each divalent cation and 0.1M MES/imidazole
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.852 α = 89.86 b = 90.898 β = 80.92 c = 92.869 γ = 75.82
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 2015-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95373 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.19 50 98.3 0.091 7.4 4 120215
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 97.5 0.571 3.7
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 2.19 40.32 114158 6057 97.39 0.1676 0.1654 0.1726 0.2069 0.2106 RANDOM 44.414
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] -0.45 -0.45 0.73 1.21 -0.43 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.323 r_dihedral_angle_4_deg 17.094 r_dihedral_angle_3_deg 15.396 r_dihedral_angle_1_deg 6.791 r_angle_refined_deg 1.858 r_angle_other_deg 0.957 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.323 r_dihedral_angle_4_deg 17.094 r_dihedral_angle_3_deg 15.396 r_dihedral_angle_1_deg 6.791 r_angle_refined_deg 1.858 r_angle_other_deg 0.957 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15579 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 240
Software Software Software Name Purpose MxCuBE data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing