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Structural basis for 5'-end-specific recognition of the guide RNA strand by the A. fulgidus PIWI protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W9H pdb entry 1w9H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG 4K, potassium chloride, magnisium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.88 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 238.747 α = 90 b = 238.747 β = 90 c = 52.042 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2005-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 0.9776 NSLS X26C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 50 99.3 0.046 0.046 38254 2 2
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 2.5 2.59 98.8 0.279
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT pdb entry 1w9H 2.5 50 2 36055 36055 1904 99.19 0.20689 0.20392 0.2026 0.26623 0.2608 RANDOM 61.463
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] -0.87 -0.44 -0.87 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.749 r_dihedral_angle_3_deg 19.923 r_dihedral_angle_4_deg 19.249 r_dihedral_angle_1_deg 7.221 r_scangle_it 3.309 r_scbond_it 2.216 r_mcangle_it 1.834 r_angle_refined_deg 1.792 r_mcbond_it 1.208 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.749 r_dihedral_angle_3_deg 19.923 r_dihedral_angle_4_deg 19.249 r_dihedral_angle_1_deg 7.221 r_scangle_it 3.309 r_scbond_it 2.216 r_mcangle_it 1.834 r_angle_refined_deg 1.792 r_mcbond_it 1.208 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.255 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.118 r_metal_ion_refined 0.059 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6814 Nucleic Acid Atoms 409 Solvent Atoms 57 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing