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Crystal structure of Glutamyl-tRNA synthetase 1 (EC 6.1.1.17) (Glutamate-tRNA ligase 1) (GluRS 1) (TM1351) from Thermotoga maritima at 2.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G59 pdb entry 1G59 Chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 8 277 0.2M CaAcetate, 10.0% PEG-8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.53 65.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.953 α = 90 b = 69.953 β = 90 c = 283.945 γ = 120
Symmetry Space Group P 31 2 1
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 MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-08-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.94926, 0.97925, 0.97939 APS 23-ID-D
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 2.34 47.351 99.9 0.165 6.6 35284 46.8
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 2.34 2.42 100 0.012 1.6 7.26 3322
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MAD, MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1G59 Chain A 2.34 47.351 30264 1524 85.96 0.236 0.234 0.2395 0.268 0.2758 RANDOM 23.855
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] -0.18 -0.09 -0.18 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.887 r_dihedral_angle_4_deg 11.053 r_dihedral_angle_3_deg 10.179 r_dihedral_angle_1_deg 3.06 r_angle_refined_deg 1.427 r_angle_other_deg 1.235 r_scangle_it 0.998 r_scbond_it 0.662 r_mcangle_it 0.528 r_mcbond_it 0.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.887 r_dihedral_angle_4_deg 11.053 r_dihedral_angle_3_deg 10.179 r_dihedral_angle_1_deg 3.06 r_angle_refined_deg 1.427 r_angle_other_deg 1.235 r_scangle_it 0.998 r_scbond_it 0.662 r_mcangle_it 0.528 r_mcbond_it 0.347 r_nbtor_refined 0.146 r_nbd_refined 0.144 r_nbd_other 0.117 r_symmetry_vdw_other 0.111 r_symmetry_vdw_refined 0.104 r_chiral_restr 0.083 r_xyhbond_nbd_refined 0.078 r_nbtor_other 0.067 r_mcbond_other 0.044 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3828 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 9
Software Software Software Name Purpose SHELX phasing SOLVE phasing MOLREP phasing RESOLVE phasing REFMAC refinement XSCALE data scaling MolProbity model building PDB_EXTRACT data extraction XDS data reduction SHELXD phasing