☰ Navigation Tabs
Crystal structure of E. coli threonyl tRNA synthetase in complex with a TM84 analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293 12% (w/v) PEG 4000, 21% (v/v) MPD, and 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.763131 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.33 α = 90 b = 108.95 β = 90 c = 113.96 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 S 16M 2022-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.05 78.75 99 0.994 9.3 2.2 45827
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.258 48 0.996
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.05 78.75 43429 2397 68.15 0.216 0.18892 0.266 0.2664 RANDOM 41.717
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] -0.5 0.18 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.056 r_dihedral_angle_3_deg 17.127 r_long_range_B_refined 8.625 r_long_range_B_other 8.589 r_dihedral_angle_1_deg 7.775 r_scangle_other 6.424 r_mcangle_it 4.927 r_mcangle_other 4.926 r_scbond_it 4.419 r_scbond_other 4.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.056 r_dihedral_angle_3_deg 17.127 r_long_range_B_refined 8.625 r_long_range_B_other 8.589 r_dihedral_angle_1_deg 7.775 r_scangle_other 6.424 r_mcangle_it 4.927 r_mcangle_other 4.926 r_scbond_it 4.419 r_scbond_other 4.418 r_mcbond_it 3.511 r_mcbond_other 3.511 r_angle_refined_deg 1.563 r_angle_other_deg 0.522 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 6560 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 39
Software Software Software Name Purpose autoPROC data processing xia2.multiplex data reduction Aimless data scaling PHASER phasing REFMAC refinement