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Crystal structure of Paromomycin bound to the yeast 80S ribosome
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 434.53 α = 90 b = 293.33 β = 97.4 c = 295.79 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 90 PIXEL DECTRIS PILATUS 6M 2015-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.0 SOLEIL PROXIMA 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 3.3 146.665 100 0.321 0.332 0.989 7.37 14.851 1098455 -3 89.79
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 3.3 3.4 99.9 1.876 2.031 0.349 0.96 6.681
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.3 146.665 1.34 1098039 21962 99.94 0.2039 0.203 0.2048 0.25 0.2507 102.7427
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 20.234 f_angle_d 0.99 f_chiral_restr 0.049 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 174773 Nucleic Acid Atoms 216058 Solvent Atoms 4 Heterogen Atoms 7150
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing