☰ Navigation Tabs
Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed with Halofuginone and AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 CrpaA.18681.a.B3.PW37711 at 21.5 mg/mlprotein was incubated with 4 mM MgCl2, halofuginone, and AMPPNP, then mixed 1:1 with Top96(a5):0.1 M HEPES:NaOH, pH = 7.5, 20% (w/v) PEG-4000, 10% (v/v) 2-propanol, harvested with 20% ethylene glycol4 mM MgCl2, halofuginone, and AMPPNP, then mixed 1:1 with Top96(a5):0.1 M HEPES:NaOH, pH = 7.5, 20% (w/v) PEG-4000, 10% (v/v) 2-propanol, harvested with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.59 52.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.4 α = 90 b = 108.72 β = 90 c = 126.35 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN 944+ 2015-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.4 50 98.4 0.105 0.119 11.07 4.3 48156 -3 31.54
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 2.4 2.46 95.5 0.573 0.662 2.6 3.7
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 FOURIER SYNTHESIS FREE R-VALUE 5F9Y 2.4 46.611 1.34 48089 2063 98.4 0.2087 0.2075 0.2093 0.2341 0.2363 37.0439
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 14.055 f_angle_d 0.486 f_chiral_restr 0.044 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7719 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 120
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing