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The crystal structure of the putative tRNA synthase from Salmonella typhimurium LT2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 0.1 M Bis/Tris, 3M NaCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.92 75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 254.541 α = 90 b = 254.541 β = 90 c = 94.459 γ = 120
Symmetry Space Group P 64 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 100 CCD ADSC QUANTUM 315 mirrors 2008-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 2.7 127 0.9987 0.158 25.71 25.1 47218 47157 2 2 40
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) 1 2.7 2.771 0.9956 0.76 2.5 22.3 3611
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.7 127 47218 47157 2515 99.87 0.18948 0.18836 0.1939 0.21048 0.2155 RANDOM 39.832
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] 1.45 0.73 1.45 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.024 r_dihedral_angle_4_deg 22.25 r_dihedral_angle_3_deg 19.386 r_dihedral_angle_1_deg 6.851 r_scangle_it 3.68 r_scbond_it 2.409 r_angle_refined_deg 1.718 r_mcangle_it 1.361 r_mcbond_it 1.148 r_angle_other_deg 1.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.024 r_dihedral_angle_4_deg 22.25 r_dihedral_angle_3_deg 19.386 r_dihedral_angle_1_deg 6.851 r_scangle_it 3.68 r_scbond_it 2.409 r_angle_refined_deg 1.718 r_mcangle_it 1.361 r_mcbond_it 1.148 r_angle_other_deg 1.014 r_symmetry_vdw_other 0.278 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.22 r_nbd_other 0.207 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.154 r_mcbond_other 0.144 r_symmetry_hbond_refined 0.104 r_nbtor_other 0.099 r_chiral_restr 0.096 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6219 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing