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Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 4A5 on the guide 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 2.6 M Na-acetate, pH 7.0, 0.1M Tris-Cl, pH 7.4 and 0.2 M glycine
Crystal Properties Matthews coefficient Solvent content 3.92 68.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.14 α = 90 b = 202.14 β = 90 c = 202.14 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 AREA DETECTOR DECTRIS PILATUS 2M-F 2014-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1000 Photon Factory BL-1A
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 3.1 50 98.9 9.7 6.6 25862
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 3.1 45.2 1.35 25862 1313 98.9 0.217 0.214 0.2176 0.276 0.2749
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 17.707 f_angle_d 1.633 f_chiral_restr 0.064 f_bond_d 0.022 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5091 Nucleic Acid Atoms 714 Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement HKL-2000 data processing HKL-2000 data scaling PHASER phasing