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The crystal structure of homodimeric E. coli tryptophanyl-tRNA synthetase bound with niraparib at one of its two active sites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 0.16M Ammonium sulfate, 0.1M HEPES pH 7.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.656 α = 90 b = 79.761 β = 106.32 c = 77.338 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL RIGAKU HyPix-6000HE 2022-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 99.9 0.121 0.052 0.994 11.1 5 42029
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.21 100 0.57 0.31 0.766 3.2
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 5V0I 2.1 50 39904 2095 99.83 0.20313 0.2015 0.2083 0.23439 0.2402 RANDOM 20.242
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] -0.83 0.24 1.36 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.928 r_dihedral_angle_4_deg 17.431 r_dihedral_angle_3_deg 11.561 r_dihedral_angle_1_deg 5.254 r_long_range_B_refined 2.324 r_long_range_B_other 2.19 r_angle_refined_deg 1.135 r_mcangle_it 0.995 r_mcangle_other 0.994 r_angle_other_deg 0.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.928 r_dihedral_angle_4_deg 17.431 r_dihedral_angle_3_deg 11.561 r_dihedral_angle_1_deg 5.254 r_long_range_B_refined 2.324 r_long_range_B_other 2.19 r_angle_refined_deg 1.135 r_mcangle_it 0.995 r_mcangle_other 0.994 r_angle_other_deg 0.875 r_scangle_other 0.845 r_mcbond_it 0.549 r_mcbond_other 0.547 r_scbond_it 0.481 r_scbond_other 0.478 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5046 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing CrysalisPro data reduction