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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 2.42 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.617 α = 90 b = 80.047 β = 105.69 c = 78.28 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 1.95 50 99.4 0.066 0.079 0.043 0.997 10.9 3.3 53051
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 1.95 2 97.5 0.374 0.454 0.255 0.936 2.9
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 1.95 50 50390 2636 99.24 0.20033 0.19926 0.2052 0.22146 0.2276 RANDOM 33.751
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] -3.46 0.32 2.7 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.56 r_dihedral_angle_4_deg 20.231 r_dihedral_angle_3_deg 12.076 r_dihedral_angle_1_deg 5.309 r_long_range_B_refined 3.702 r_long_range_B_other 3.702 r_scangle_other 2.287 r_mcangle_it 2.007 r_mcangle_other 2.007 r_scbond_it 1.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.56 r_dihedral_angle_4_deg 20.231 r_dihedral_angle_3_deg 12.076 r_dihedral_angle_1_deg 5.309 r_long_range_B_refined 3.702 r_long_range_B_other 3.702 r_scangle_other 2.287 r_mcangle_it 2.007 r_mcangle_other 2.007 r_scbond_it 1.359 r_scbond_other 1.359 r_mcbond_it 1.222 r_mcbond_other 1.219 r_angle_refined_deg 1.198 r_angle_other_deg 0.899 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 5068 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing XDS data reduction