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Leishmania donovani tyrosyl-tRNA synthetase in complex with nanobody and inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 298 0.1 M sodium cacodylate pH 5.7, 22% PEG 4,000, vapor diffusion, sitting drop, temperature 298
Crystal Properties Matthews coefficient Solvent content 2.67 53.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.18 α = 90 b = 96.18 β = 90 c = 351.83 γ = 120
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 PSI PILATUS 6M 2015-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.98 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.75 83.29 100 0.21 0.995 8.7 10.3 47547
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3P0J 2.75 83.29 45156 2311 99.81 0.19144 0.18886 0.1901 0.24353 0.2419 RANDOM 65.26
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] -0.22 -0.11 -0.22 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.849 r_dihedral_angle_4_deg 17.169 r_dihedral_angle_3_deg 14.213 r_long_range_B_refined 9.338 r_long_range_B_other 9.338 r_scangle_other 6.308 r_mcangle_it 5.81 r_mcangle_other 5.809 r_dihedral_angle_1_deg 5.666 r_scbond_it 3.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.849 r_dihedral_angle_4_deg 17.169 r_dihedral_angle_3_deg 14.213 r_long_range_B_refined 9.338 r_long_range_B_other 9.338 r_scangle_other 6.308 r_mcangle_it 5.81 r_mcangle_other 5.809 r_dihedral_angle_1_deg 5.666 r_scbond_it 3.869 r_scbond_other 3.868 r_angle_other_deg 3.75 r_mcbond_it 3.676 r_mcbond_other 3.676 r_angle_refined_deg 1.438 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 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 12283 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement Aimless data scaling HKL-2000 data scaling PHASER phasing