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50S Deinococcus radiodurans ribosome bounded with mycinamicin IV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293.15 Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Crystal Properties Matthews coefficient Solvent content 4.78 74.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.59 α = 90 b = 410.128 β = 90 c = 690.477 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2017-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.968 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50.074 97.3 0.295 0.323 0.128 7.3 5 344576
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.36 95.3 0.92 1.049 0.483 0.443 3.8
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 THROUGHOUT 3PIO 3.4 50 1.33 307913 15317 93.94 0.2854 0.2837 0.295 0.3182 0.329 109.0173
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23436 Nucleic Acid Atoms 60533 Solvent Atoms Heterogen Atoms 396
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing