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Crystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 310 50 mM Na Cacodylate (pH 6.4), 150 mM KCl, 1% Glycerol, 1% 2-methyl-2,4-pentandiol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal Properties Matthews coefficient Solvent content 2.79 55.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.49 α = 90 b = 43.02 β = 90 c = 98.75 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2005-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
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 1.8 32.4 100 0.07 19.1 14605
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) 1.8 1.9 0.609 11.2
Refinement Statistics Diffraction ID Structure Solution 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 1J7T 1.8 32 14603 2272 99.9 0.211 0.2124 0.243 0.2427 random 37.822
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] -2.204 2.918 -0.714
RMS Deviations Key Refinement Restraint Deviation c_mcangle_it 2.38 c_mcbond_it 1.664 c_improper_angle_d 1.3 c_angle_deg 0.9 c_bond_d 0.006 c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 900 Solvent Atoms 206 Heterogen Atoms 180
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling AMoRE phasing