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Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U on the Ribosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I9D PDB ENTRY 3I9D AND 3I9E experimental model PDB 3I9E PDB ENTRY 3I9D AND 3I9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 4% PEG 20k, 4% PEG550 MME, 0.1M TRIS-ACETATE, 0.2M KSCN, 10mM MgCl, pH 7.0, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.33 63.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.2 α = 90 b = 450.23 β = 90 c = 621.74 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 CCD ADSC QUANTUM 315 2012-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.18 34.966002 98.5 0.249 7.88 962803 962803 -3 -3 67.128
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.18 3.26 98.2 0.016 1.08
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 FOURIER SYNTHESIS PDB ENTRY 3I9D AND 3I9E 3.22000098079 34.9660015924 1.99114820421 927241 43371 98.5416020167 0.23075614842 0.22935560927 0.2288 0.259831070518 0.259 RANDOM 6.58651201936
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 17.4063209199 f_angle_d 1.10063403034 f_chiral_restr 0.0640124896678 f_plane_restr 0.00761540016734 f_bond_d 0.00589029866773
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 93008 Nucleic Acid Atoms 198180 Solvent Atoms Heterogen Atoms 769
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction