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Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HK2 PDB ENTRY 3HK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 308 80 mM MgCl2, 1.0 M Na tartrate, 50 mM Tris.HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 308 K
Crystal Properties Matthews coefficient Solvent content 3.11 60.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.252 α = 90 b = 116.903 β = 90 c = 170.504 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 MARMOSAIC 300 mm CCD 2009-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
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 3.2 50 95.2 0.12 15 4.9 34970 -1 95.75
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 3.2 3.31 88.9 0.412 1.5 3.5 3220
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3HK2 3.211 37.68 0.13 34940 1743 94.41 0.229 0.226 0.273 0.2496 RANDOM 97.522
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] 3.626 8.149 -11.775
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.216 f_angle_d 1.111 f_chiral_restr 0.071 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9513 Nucleic Acid Atoms 1108 Solvent Atoms Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing