☰ Navigation Tabs
N-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase (Tbxo4 derivative crystal structure)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Stock protein concentration: 6-9 mg/mL
Well solution: 0.1 M HEPES-NaOH pH 7.5, 1.4-1.5 M ammonium sulfate, 10-20% (vol) glycerol
Mix: 400 nL protein solution/seeds + 400 nL well solution
Use of microseeding technique to improve crystal size.
1 microliter of a 100 mM Tbxo4 solution (ligand code 7MT) was added to the crystallization drop for a soacking of 1-2 minutes before freezing the crystals.
Crystal Properties Matthews coefficient Solvent content 3.16 61.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.11 α = 90 b = 88.51 β = 105.7 c = 168.64 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 PIXEL DECTRIS EIGER X 16M Kirkpatrick-Baez bimorphic mirrors 2020-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.631371 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.17 47.85 99.83 0.1229 0.1259 0.0272 1 14.87 21.2 61436 129
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 3.17 3.283 99.47 2.335 2.395 0.5287 0.789 1.13 19.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 3.17 47.85 1.34 61359 3073 99.86 0.1942 0.192 0.1935 0.2373 0.2361 169.93
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 11.8889 f_angle_d 0.5832 f_chiral_restr 0.0473 f_plane_restr 0.0041 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8125 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 71
Software Software Software Name Purpose PHENIX refinement CRANK2 phasing XSCALE data scaling XDS data reduction MxCuBE data collection