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Crystal structure of the Thermus thermophilus 70S ribosome in complex with plazomicin, mRNA and tRNAs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V51
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 100 mM TRIS-HCl, pH 7.6,
3-3.2% (w/v) PEG 20K,
7-12% (v/v) MPD,
100-200 mM arginine,
0.5 mM Beta-mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 3.3 62.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.45 α = 90 b = 449.379 β = 90 c = 619.589 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 PILATUS3 6M 2019-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97857 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.268 147.06 99.67 0.986 5.94 6.5 890586 85.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.268 3.385 97.48 0.462 5.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 4V51 3.27 147.06 1.33 890059 44294 99.67 0.2171 0.214 0.2148 0.2767 0.2763 86.82
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 17.4129 f_angle_d 1.8152 f_chiral_restr 0.0766 f_bond_d 0.0117 f_plane_restr 0.0102
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 95669 Nucleic Acid Atoms 199314 Solvent Atoms 2 Heterogen Atoms 1464
Software Software Software Name Purpose PHENIX refinement MxDC data collection xia2 data scaling Coot model building DIALS data reduction PHENIX phasing