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Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J7T PDB ENTRY 1J7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 310 MPD, sodium cacodylate, sodium chloride, potassium chloride, magnesium sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal Properties Matthews coefficient Solvent content 2.59 52.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.9 α = 90 b = 32.8 β = 107.9 c = 52 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 4 double crystal monochromator and toroidal focusing mirrors 2001-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.54 10 95.9 0.059 19.5 4.8 4899 62.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.64 98.4 0.133 9.2 4.7 479
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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-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 1J7T 2.54 10 1.5 4899 4644 396 91.9 0.214 0.2139 0.264 0.2604 random 61.4
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 c_dihedral_angle_d 9.71789 c_angle_deg 1.03474 c_improper_angle_d 0.75231 c_bond_d 0.005567
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 898 Solvent Atoms 76 Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement