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Crystal structure of the editing domain of E. coli leucyl-tRNA synthetase complexes with isoleucine
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 = 112.487 α = 90 b = 112.487 β = 90 c = 135.023 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 2005-01-01 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 3.2 50 89.4 0.091 8.7 4.4 8642 7726
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) 3.2 3.37 89.4 0.41 2.1 4.4 1086
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 3.2 20 7329 7329 363 87.82 0.23436 0.23436 0.23196 0.2318 0.2836 0.2361 RANDOM 55.124
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] 2.21 1.1 2.21 -3.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.103 r_scangle_it 2.039 r_angle_refined_deg 1.17 r_scbond_it 1.105 r_mcangle_it 0.99 r_mcbond_it 0.522 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.103 r_scangle_it 2.039 r_angle_refined_deg 1.17 r_scbond_it 1.105 r_mcangle_it 0.99 r_mcbond_it 0.522 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 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 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement CNS phasing