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Crystal Structure of E.coli Arginyl-tRNA Synthetase and Ligand Binding Studies Revealed Key Residues in Arginine Recognition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BS2 1BS2 as ensemble 1 and 3GDZ as ensemble 2 experimental model PDB 3GDZ 1BS2 as ensemble 1 and 3GDZ as ensemble 2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 289 10mg/ml protein sample in 20 mM Tris, pH 7.5, reservior solution - 50mM HEPES (pH 7.2), 100mM sodium acetate, 22% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.53 51.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.599 α = 90 b = 94.136 β = 110.53 c = 62.717 γ = 90
Symmetry Space Group C 1 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 90 CCD ADSC QUANTUM 315 2013-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 50 99.5 20541 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 50
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1BS2 as ensemble 1 and 3GDZ as ensemble 2 2.574 35.906 1.34 20371 20270 1045 98.68 0.278 0.2049 0.2008 0.2081 0.278 0.2782 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.794 f_angle_d 1.25 f_chiral_restr 0.047 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4247 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement CNS refinement HKL-2000 data collection DENZO data reduction HKL-2000 data scaling CNS phasing