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Recognition of the amber stop codon by release factor RF1.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F1E PDB ENTRIES 3F1E and 3F1F experimental model PDB 3F1F PDB ENTRIES 3F1E and 3F1F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295.5 crystals were grown by the sitting-drop vapor diffusion method dispensed robotically using 1-2 uL ribosome complexes mixed with 1-2 uL reservoir solution (100 mM Tris-OAc, pH 7.0, 200 mM KSCN, 3.4-4.8% PEG20,000, 2.5-11.5% PEG200) at 22.5 C, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K
Crystal Properties Matthews coefficient Solvent content 3.339 61.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.38 α = 90 b = 452.7 β = 90 c = 617.09 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 2009-08-05 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D 2 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.514 89 100 724157 723953 1.1
Refinement Statistics Diffraction ID Structure Solution 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRIES 3F1E and 3F1F 3.62 49.953 1.99 663328 13271 99.99 0.26 0.26 0.2515 0.291 0.285 2% random
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 18.407 f_angle_d 0.659 f_chiral_restr 0.041 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21924 Nucleic Acid Atoms 34121 Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction CrystalClear data collection CNS refinement XDS data reduction CNS phasing