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Crystal structure of the editing domain of E. coli leucyl-tRNA synthetase
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 = 111.489 α = 90 b = 111.489 β = 90 c = 136.764 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 2005-02-16 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 50 98.6 0.072 7.8 5.3 34371 33890
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 2.07 98.3 0.406 1.7 5.5 3377
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 20 32157 32157 1710 98.66 0.21737 0.21737 0.21573 0.2211 0.24871 0.2195 RANDOM 41.008
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] 1.33 0.66 1.33 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.478 r_scangle_it 4.219 r_scbond_it 2.366 r_mcangle_it 1.548 r_angle_refined_deg 1.177 r_mcbond_it 0.774 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.185 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.478 r_scangle_it 4.219 r_scbond_it 2.366 r_mcangle_it 1.548 r_angle_refined_deg 1.177 r_mcbond_it 0.774 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.185 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 2731 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CNS phasing