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Crystal structure of the Thermus thermophilus 70S ribosome in complex with antibiotic A201A, mRNA and three tRNAs in the A, P and E sites at 2.65A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y4P
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, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME
Crystal Properties Matthews coefficient Solvent content 2.89 57.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.89 α = 90 b = 446.22 β = 90 c = 619.48 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 2014-10-11 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) 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 2.65 362.069 98.5 0.15 6.34 3.469 1628435 -3 50.72
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 2.65 2.72 99.3 1.203 1.03
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4Y4P 2.65 362.069 1.34 1628316 81733 98.5 0.228 0.226 0.271 0.2612 59.02
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 15.055 f_angle_d 0.945 f_chiral_restr 0.04 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 91002 Nucleic Acid Atoms 202018 Solvent Atoms 3713 Heterogen Atoms 2436
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction