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The asymmetric structure of homodimeric E. coli TrpRS bound with tryptophanyl adenylate at one of its two active pockets
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 2.39 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.68 α = 90 b = 79.68 β = 106.04 c = 77.65 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 1.8 50 98.8 0.061 0.067 0.027 0.998 18.2 6.5 65978
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 1.8 1.84 98.3 0.483 0.523 0.199 0.971 6.9
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 1.8 50 62587 3372 98.51 0.18772 0.18594 0.1943 0.22171 0.2257 RANDOM 30.285
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] -3.34 0.85 1.05 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.467 r_dihedral_angle_4_deg 15.611 r_dihedral_angle_3_deg 11.615 r_dihedral_angle_1_deg 5.228 r_long_range_B_refined 3.236 r_long_range_B_other 3.103 r_scangle_other 1.789 r_mcangle_it 1.525 r_mcangle_other 1.522 r_angle_refined_deg 1.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.467 r_dihedral_angle_4_deg 15.611 r_dihedral_angle_3_deg 11.615 r_dihedral_angle_1_deg 5.228 r_long_range_B_refined 3.236 r_long_range_B_other 3.103 r_scangle_other 1.789 r_mcangle_it 1.525 r_mcangle_other 1.522 r_angle_refined_deg 1.148 r_scbond_it 1.074 r_scbond_other 1.068 r_mcbond_it 0.915 r_mcbond_other 0.912 r_angle_other_deg 0.867 r_chiral_restr 0.062 r_bond_refined_d 0.006 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 5094 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 57
Software Software Software Name Purpose Aimless data scaling REFMAC refinement XDS data reduction MOLREP phasing