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Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-A 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 3.31 62.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.241 α = 90 b = 446.1 β = 90 c = 623.316 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 2012-02-20 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 3.7 49.676 99.1 0.313 4.51 612965 612965 -3 -3 85.008
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 3.7 3.8 99.7 0.014 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 3.90000100875 49.6753690821 1.99156751478 523517 23225 99.0419632942 0.237079404994 0.235177200017 0.2347 0.278294847635 0.278 RANDOM 6.62923505921
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 17.5229832134 f_angle_d 1.20147228824 f_chiral_restr 0.0664835743966 f_plane_restr 0.00767553124034 f_bond_d 0.00659915224506
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 93000 Nucleic Acid Atoms 198184 Solvent Atoms Heterogen Atoms 766
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction