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Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 at 21.9mg/ml, incubated with 5mM TCMDC-124506, then 1:1 with Morpheus(B2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each magnesium chloride, calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.45 49.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.18 α = 90 b = 91.34 β = 129.53 c = 110.91 γ = 90
Symmetry Space Group C 1 2 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 RAYONIX MX-225 2014-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.979490 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.65 50 97.2 0.049 0.056 16.31 4.1 133468 -3 21.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 96.2 0.539 0.615 3.01 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4Q15 1.65 40.288 1.34 133461 2133 97.56 0.162 0.1616 0.1629 0.1879 0.1884 33.2662
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.426 f_angle_d 1.047 f_chiral_restr 0.044 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7035 Nucleic Acid Atoms Solvent Atoms 766 Heterogen Atoms 124
Software Software Software Name Purpose ARP model building PHENIX refinement PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing