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Crystal structure of the dolphin proline-rich antimicrobial peptide Tur1A bound to the Thermus thermophilus 70S ribosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293 Tris-HCl pH 7.6, PEG 20,000, 2-methyl-2,4-pentanediol, L-arginine
Crystal Properties Matthews coefficient Solvent content 3.43 64.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.68 α = 90 b = 449.25 β = 90 c = 621.9 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 2016-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972422 ESRF ID23-1
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 3.2 49.757 98.6 0.393 0.423 0.98 4.08 7.058 941634 75.88
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 3.2 3.28 98.6 1.902 2.045 0.323 1 7.246
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 5F8K 3.2 49.757 1.35 941410 47069 98.58 0.1929 0.1898 0.1905 0.2516 0.25 57.9
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 16.663 f_angle_d 1.978 f_chiral_restr 0.084 f_bond_d 0.03 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 93386 Nucleic Acid Atoms 193386 Solvent Atoms Heterogen Atoms 7522
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing