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Crystal structure of the Thermus thermophilus 70S ribosome bound to translation inhibitor oncocin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.6 292 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.9% PEG-20K, 7-12% MPD, 0.5 mM BME
Crystal Properties Matthews coefficient Solvent content 3.35 58.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.14 α = 90 b = 450.73 β = 90 c = 623.47 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 PIXEL DECTRIS PILATUS 6M-F S/N 60-0112-F 2014-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97900 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.8 60 98.2 0.185 0.213 7.03 3.848 1433648 1407992 1 -3 61.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 94 2.112 2.466 0.66
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 59.981 1.34 1271909 63740 98.51 0.2051 0.2029 0.2039 0.2476 0.2475 59.85
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 15.108 f_angle_d 0.717 f_chiral_restr 0.032 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 90537 Nucleic Acid Atoms 191485 Solvent Atoms 1201 Heterogen Atoms 5155
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction