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80S yeast ribosome in complex with Fluorolissoclimide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V88
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Crystal Properties Matthews coefficient Solvent content 3.21 61.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 303.68 α = 90 b = 287.58 β = 98.93 c = 435.09 γ = 90
Symmetry Space Group P 1 21 1
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 16M 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.9 207.6 99.69 0.09 0.13 0.094 0.994 25.4 12 3210225 76.98
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 2.9 3 0.12 0.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.9 207.6 3198596 99.53 0.2203 0.2202 0.2324 0.223 0.2541
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_angle_d 1.305 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 174883 Nucleic Acid Atoms 221181 Solvent Atoms 231 Heterogen Atoms 8606
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing