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The structure of amicetin bound to the 70S ribosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y4O PDB entry 4Y4O without YfiA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 292 0.1-0.2 M arginine-HCl, 0.1 M Tris-HCl, pH 7.6, 2.5% PEG20000, 7-12% MPD, 0.5 mM BME
Crystal Properties Matthews coefficient Solvent content 3.07 64.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.04 α = 90 b = 449.52 β = 90 c = 624.08 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 PILATUS 6M 2014-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.979 NSLS X25
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 3.14 49.916 71.8 0.329 0.38 0.942 3.28 3.54 1001501 74.56
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 4.7 4.82 66.6 1.196 1.435 0.261 0.97 2.732
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 PDB entry 4Y4O without YfiA 3.14 49.916 1.33 994190 49899 97.83 0.2412 0.2384 0.2385 0.292 0.2918 108.7499
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 13.694 f_angle_d 0.508 f_chiral_restr 0.03 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 91503 Nucleic Acid Atoms 193348 Solvent Atoms 1139 Heterogen Atoms 4644
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASES phasing