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Crystal structure of the editing domain of E. coli leucyl-tRNA synthetase complexes with methionine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 (NH4)2SO4, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.518 α = 90 b = 111.518 β = 90 c = 134.931 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 IMAGE PLATE RIGAKU RAXIS IV osmic mirror 2005-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 50 98.9 0.121 4.5 6.2 20004 19784
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 99.7 0.452 1.4 6 1941
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.4 20 18755 18755 1007 98.8 0.24331 0.24331 0.24108 0.2418 0.28432 0.2555 RANDOM 52.614
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] 2.33 1.17 2.33 -3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.149 r_scangle_it 3.922 r_scbond_it 2.408 r_mcangle_it 1.583 r_angle_refined_deg 1.474 r_mcbond_it 0.815 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.22 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.149 r_scangle_it 3.922 r_scbond_it 2.408 r_mcangle_it 1.583 r_angle_refined_deg 1.474 r_mcbond_it 0.815 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.22 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2693 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement CNS phasing