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Trypanosoma cruzi Lysyl-tRNA synthetase in complex with L-Lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HCU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1 M HEPES pH 7.5; 0.4 M Sodium acetate; 28% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.967 α = 90 b = 59.967 β = 90 c = 310.338 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS 2M 2025-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.9772 LNLS SIRIUS MANACA
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 2.08 47.45 99.8 0.156 0.159 0.043 0.998 14.3 25.1 35668 0.46 47.78
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 2.08 2.13 97.5 2.999 3.061 0.606 0.456 1.5 24.8
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 (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 2.08 47.45 33768 1780 99.8 0.196 0.193 0.2002 0.246 0.2423 RANDOM 62.14
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 1 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.511 r_long_range_B_other 11.803 r_long_range_B_refined 11.793 r_dihedral_angle_2_deg 10.757 r_scangle_other 9.592 r_dihedral_angle_1_deg 7.87 r_mcangle_it 7.684 r_mcangle_other 7.682 r_scbond_it 7.059 r_scbond_other 7.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.511 r_long_range_B_other 11.803 r_long_range_B_refined 11.793 r_dihedral_angle_2_deg 10.757 r_scangle_other 9.592 r_dihedral_angle_1_deg 7.87 r_mcangle_it 7.684 r_mcangle_other 7.682 r_scbond_it 7.059 r_scbond_other 7.057 r_mcbond_it 5.831 r_mcbond_other 5.831 r_angle_refined_deg 2.116 r_angle_other_deg 0.692 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3955 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction