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Structure of Thermus thermophilus Argonaute bound to guide DNA and 19-mer target DNA with Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HM9 PDB ENTRY 3HM9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 306 18 mM magnesium chloride, 9% isopropanol, 50 mM sodium cacodylate, pH 6.5, 2.25 mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 306K
Crystal Properties Matthews coefficient Solvent content 2.27 45.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.736 α = 90 b = 105.363 β = 94.25 c = 92.058 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2012-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97 SSRF BL17U
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 2.189 50 91.2 0.073 12.9 2.8 75224 32.7
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 2.189 2.24 88.6 0.455 2.4 3666
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 ENTRY 3HM9 2.189 39.216 1.4 75196 75196 3787 90.6 0.1776 0.1748 0.1755 0.2296 0.2293 RANDOM 35.5953
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 18.536 f_angle_d 1.115 f_chiral_restr 0.069 f_bond_d 0.009 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10515 Nucleic Acid Atoms 1417 Solvent Atoms 444 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection PHASER phasing