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Crystal Structure of the 70S ribosome with tetracycline.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UZ6 PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9 experimental model PDB 3UZ7 PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9 experimental model PDB 3UZ8 PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9 experimental model PDB 3UZ9 PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 4% PEG20K, 4% PEGMME 550, 100mM Tris/HAc, 200mM KSCN, pH 7.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.31 62.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.27 α = 90 b = 448.54 β = 90 c = 615.75 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 PIXEL PSI PILATUS 6M 2012-02-11 M SINGLE WAVELENGTH 2 1 x-ray 100 M SINGLE WAVELENGTH 3 1 x-ray 100 M SINGLE WAVELENGTH 4 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 1,2,3,4 3.2999 300 100 0.423 10.71 45.3 859994 859965 -3 -3 119.815
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 PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9 3.2999 173.073 1.33 859994 859870 2000 99.98 0.2026 0.2026 0.2024 0.1981 0.2539 0.2511 RANDOM 148.1456
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] -23.2791 8.6238 14.6553
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.711 f_angle_d 0.682 f_chiral_restr 0.057 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19203 Nucleic Acid Atoms 34094 Solvent Atoms Heterogen Atoms 955
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction RemDAq data collection PHENIX model building XDS data reduction PHENIX phasing