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Crystal structure of the Candida albicans 80S ribosome in complex with Paromomycin (250uM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277.15 PEG 20K, KSCN, Mg Acetate, K - acetate, Bis-Tris-Acetate, Glycerol, Spermidine, phyllanthoside
Crystal Properties Matthews coefficient Solvent content 3.24 62.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 298.32 α = 90 b = 293.37 β = 100.16 c = 451.08 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 173 PIXEL DECTRIS EIGER X 16M 2022-04-10 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 3.3 177.03 99.3 0.695 0.721 0.1885 0.992 4.36 14.4 1134400 87.83
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 3.35 3.3819999999999997 3.503 0.052000000000000005
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 3.3 177.03 1.33 1133838 1824 99.29 0.2542 0.2541 0.254 0.2975 0.2958
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 16.484 f_angle_d 1.012 f_chiral_restr 0.054 f_plane_restr 0.007 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 181142 Nucleic Acid Atoms 222314 Solvent Atoms Heterogen Atoms 1969
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHENIX phasing