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E. coli tryptophanyl-tRNA synthetase bound with a chemical fragment at the dimerization interface
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 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.741 α = 90 b = 80.539 β = 106.3 c = 77.258 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 100 PIXEL DECTRIS PILATUS3 6M 2020-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
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 2.35 50 99.5 0.126 0.151 0.081 0.99 7 3.4 30223
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 2.35 2.44 99.6 0.614 0.732 0.395 0.744 3.3
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 2.35 50 28710 1495 99.33 0.21578 0.21429 0.2189 0.24408 0.2447 RANDOM 35.589
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] -1.19 0.34 2.64 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.279 r_dihedral_angle_4_deg 16.283 r_dihedral_angle_3_deg 12.963 r_dihedral_angle_1_deg 5.18 r_long_range_B_refined 2.048 r_long_range_B_other 2.048 r_mcangle_it 1.159 r_mcangle_other 1.158 r_angle_refined_deg 1.102 r_angle_other_deg 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.279 r_dihedral_angle_4_deg 16.283 r_dihedral_angle_3_deg 12.963 r_dihedral_angle_1_deg 5.18 r_long_range_B_refined 2.048 r_long_range_B_other 2.048 r_mcangle_it 1.159 r_mcangle_other 1.158 r_angle_refined_deg 1.102 r_angle_other_deg 0.87 r_scangle_other 0.819 r_mcbond_it 0.627 r_mcbond_other 0.626 r_scbond_it 0.432 r_scbond_other 0.432 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 5011 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 62
Software Software Software Name Purpose Aimless data scaling MOLREP phasing REFMAC refinement XDS data reduction