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Crystal structure of ASL-Thr bound to Codon ACC-A on the Ribosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I8F 3I8F, 3I8G, 3I8H, 3I8I experimental model PDB 3I8G 3I8F, 3I8G, 3I8H, 3I8I experimental model PDB 3I8H 3I8F, 3I8G, 3I8H, 3I8I experimental model PDB 3I8I 3I8F, 3I8G, 3I8H, 3I8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 4% PEG 20k, 4% PEG550 MME, 0.1M TRIS-ACETATE, 0.2M KSCN, 10mM MgCl
Crystal Properties Matthews coefficient Solvent content 3.3 62.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.977 α = 90 b = 448.713 β = 90 c = 621.01 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 PSI PILATUS 6M 2013-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.4 70 98.2 0.256 0.293 5.99 4.1 778870 -3 82.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.5 99.4 1.329 1.524 1.21
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 FREE R-VALUE 3I8F, 3I8G, 3I8H, 3I8I 3.6 68.592 1.35 656584 29744 98.22 0.2095 0.2075 0.2097 0.2518 0.252 83.86
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 17.22 f_angle_d 1.007 f_chiral_restr 0.055 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 93003 Nucleic Acid Atoms 198250 Solvent Atoms Heterogen Atoms 1058
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction