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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with pleuromutilin-18 triazole derivative and protein Y at 2.90A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XHX
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 3.4 63.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.38 α = 90 b = 452.11 β = 90 c = 624.5 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 EIGER X 9M S/N E-18-0104 2024-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 1.033202 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.9 366.21 99.5 0.284 0.324 0.97 5.43 4.349 1291995 48.276
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.98 99.3 1.605 1.823 0.166 0.95 4.478
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 MOLECULAR REPLACEMENT FREE R-VALUE 6XHX 2.9 366.21 1.33 1290355 64709 99.34 0.2159 0.2132 0.2123 0.2666 0.2639 56.6486
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 16.651 f_angle_d 0.834 f_chiral_restr 0.041 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 93012 Nucleic Acid Atoms 193349 Solvent Atoms 8512 Heterogen Atoms 2588
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement Coot model building PDB_EXTRACT data extraction