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Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 6'A7' on the target strand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 308 2.0 M Na-formate and 0.1 M Tris-HCl pH 7.2-7.5
Crystal Properties Matthews coefficient Solvent content 3.91 68.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.824 α = 90 b = 200.824 β = 90 c = 200.824 γ = 90
Symmetry Space Group P 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 315r 2015-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 50 99.3 15.8 8.8 30962
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 2.9 2.95 99 0.528 2.1 5.9
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 4KPY 2.902 48.707 1.47 30962 1563 99.29 0.2164 0.2143 0.2187 0.2566 0.2524
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 17.161 f_angle_d 1.476 f_chiral_restr 0.065 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5241 Nucleic Acid Atoms 798 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement HKL-2000 data processing HKL-2000 data scaling PHASER phasing