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Crystal structure of Cryptosporidium parvum - Trypanosoma cruzi mutant lysyl tRNA synthetase in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ELO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein buffer: 25 mM HEPES, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP, pH 7, 30 mg/ml
Reservoir: 0.2 M Li2SO4, 14-18% PEG3350, 0.1 M tris pH 7.4-7.8
Crystal Properties Matthews coefficient Solvent content 2.56 52.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.136 α = 90 b = 116.697 β = 90 c = 142.882 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS EIGER2 X 16M 2022-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 58.35 99.7 0.082 0.033 0.999 16 13.1 160925 19.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 95 1.212 0.635 0.628 1.6 8.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 58.35 160837 8146 99.697 0.185 0.184 0.1933 0.2083 0.217 22.787
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] 0.063 0.809 -0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.226 r_dihedral_angle_3_deg 12.55 r_dihedral_angle_2_deg 9.752 r_dihedral_angle_1_deg 6.894 r_lrange_it 6.138 r_lrange_other 6.113 r_scangle_it 5.137 r_scangle_other 5.136 r_scbond_it 3.466 r_scbond_other 3.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.226 r_dihedral_angle_3_deg 12.55 r_dihedral_angle_2_deg 9.752 r_dihedral_angle_1_deg 6.894 r_lrange_it 6.138 r_lrange_other 6.113 r_scangle_it 5.137 r_scangle_other 5.136 r_scbond_it 3.466 r_scbond_other 3.464 r_mcangle_it 2.909 r_mcangle_other 2.909 r_dihedral_angle_other_2_deg 2.469 r_mcbond_it 2.132 r_mcbond_other 2.132 r_angle_refined_deg 1.857 r_angle_other_deg 0.647 r_symmetry_nbd_refined 0.247 r_nbd_refined 0.216 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.179 r_nbd_other 0.153 r_symmetry_xyhbond_nbd_other 0.142 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.107 r_ncsr_local_group_1 0.088 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8031 Nucleic Acid Atoms Solvent Atoms 754 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing