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Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Toxoplasma gondii
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 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.68 α = 90 b = 86.43 β = 106.46 c = 97.16 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2015-05-06 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) Rrim I (All) Rpim 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 2.48 53.41 99 0.159 0.054 0.997 13.6 8.5 42796
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.57 95.9 1.495 0.517 0.575 8.2
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 2.48 53.41 40574 2153 98.67 0.1962 0.1933 0.1952 0.2495 0.2524 RANDOM 44.632
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] -1.25 0.87 0.47 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.299 r_dihedral_angle_4_deg 18.046 r_dihedral_angle_3_deg 16.664 r_dihedral_angle_1_deg 6.611 r_angle_refined_deg 1.535 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7631 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 7
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing XDS data reduction SCALA data reduction