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The structure of E. coli TrpRS bound with a chemical fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V0I
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 2.43 49.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.69 α = 90 b = 79.97 β = 105.79 c = 78.54 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 EIGER X 16M 2022-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9792 SSRF BL02U1
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 1.78 50 99.8 0.05 0.055 0.022 0.999 18.4 6 70259
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 1.78 1.82 98.6 0.646 0.744 0.361 0.852 4.1
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 1.78 50 66833 3404 99.8 0.19148 0.18982 0.1974 0.22428 0.2309 RANDOM 29.447
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] -2.85 0.34 3.47 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.232 r_dihedral_angle_4_deg 16.071 r_dihedral_angle_3_deg 11.286 r_dihedral_angle_1_deg 5.67 r_long_range_B_refined 3.857 r_long_range_B_other 3.683 r_scangle_other 2.395 r_mcangle_it 1.912 r_mcangle_other 1.909 r_scbond_it 1.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.232 r_dihedral_angle_4_deg 16.071 r_dihedral_angle_3_deg 11.286 r_dihedral_angle_1_deg 5.67 r_long_range_B_refined 3.857 r_long_range_B_other 3.683 r_scangle_other 2.395 r_mcangle_it 1.912 r_mcangle_other 1.909 r_scbond_it 1.514 r_scbond_other 1.506 r_angle_other_deg 1.415 r_mcbond_it 1.233 r_mcbond_other 1.233 r_angle_refined_deg 1.217 r_chiral_restr 0.064 r_gen_planes_refined 0.005 r_bond_refined_d 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 5087 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 72
Software Software Software Name Purpose Aimless data scaling REFMAC refinement XDS data reduction MOLREP phasing