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Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 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 2.8 M Na-acetate, pH7.0, 0.1M Tris-Cl, pH 8.0 and 0.15 M glycine
Crystal Properties Matthews coefficient Solvent content 3.8 67.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.843 α = 90 b = 201.843 β = 90 c = 201.843 γ = 90
Symmetry Space Group P 21 3
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 PILATUS3 S 6M 2017-01-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 SSRF BL19U1
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 3.32 50 100 0.106 45.5 33.8 40665
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 3.32 3.38 100 0.908 4.2 26.4
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 3.33 48.95 2.15 37315 1846 92.1 0.254 0.252 0.2528 0.294 0.292
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 24.689 f_angle_d 1.703 f_chiral_restr 0.144 f_bond_d 0.013 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10369 Nucleic Acid Atoms 1470 Solvent Atoms 3 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement HKL-2000 data processing HKL-2000 data scaling PHASER phasing