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Nonamer RNA bound to hAgo2-PAZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SI3 Protein model used
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.936 α = 90 b = 91.936 β = 90 c = 69.579 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 PIXEL DECTRIS EIGER X 9M 2018-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9184 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.41 26.55 100 0.091 0.986 31.5 19.3 13092 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.5 100 1.026 0.226 0.887 3 20.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.41 26.55 12373 670 99.69 0.21836 0.21489 0.2243 0.28369 0.2856 RANDOM 68.206
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] -0.25 -0.13 -0.25 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.322 r_long_range_B_other 14.814 r_long_range_B_refined 14.794 r_scangle_other 10.166 r_dihedral_angle_1_deg 8.206 r_mcangle_it 7.901 r_mcangle_other 7.899 r_dihedral_angle_2_deg 7.879 r_scbond_it 6.626 r_scbond_other 6.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.322 r_long_range_B_other 14.814 r_long_range_B_refined 14.794 r_scangle_other 10.166 r_dihedral_angle_1_deg 8.206 r_mcangle_it 7.901 r_mcangle_other 7.899 r_dihedral_angle_2_deg 7.879 r_scbond_it 6.626 r_scbond_other 6.624 r_mcbond_it 5.411 r_mcbond_other 5.404 r_angle_refined_deg 1.464 r_angle_other_deg 0.459 r_chiral_restr 0.061 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1979 Nucleic Acid Atoms 353 Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing