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Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human anti-codon stem loop (HASL) of transfer RNA lysine 3 (tRNALys3) bound to an mRNA with an AAA-codon in the A-site and Paromomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J5E PDB entry 1J5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 MPD, NH4Cl, KCl, CaCl2, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.52 72.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 402.3 α = 90 b = 402.3 β = 90 c = 175.25 γ = 90
Symmetry Space Group P 41 21 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 2005-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97 ESRF ID14-4
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 3.1 50 98 257375 252120 2
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1J5E 3.11 29.72 252120 12418 99 0.247 0.2508 0.276 0.2541 Same set as in 1J5E extended 68.938
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] -6.5 -6.5 13.01
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.6 c_improper_angle_d 1.64 c_angle_deg 1.4 c_bond_d 0.007 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19229 Nucleic Acid Atoms 32829 Solvent Atoms Heterogen Atoms 229
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling CNS phasing