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RNA decamer duplex with eight 2'-5'-linkages
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MSB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 40 mM sodium cacodylate buffer (pH 7.0), 10% (v/v) MPD (2-methyl-2,4-pentanediol), 12 mM spermine tetrahydrochloride, 40 mM LiCl, 80 mM SrCl2 and 20 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 1.94 36.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.82 α = 90 b = 47.02 β = 96.52 c = 42.88 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2015-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000 ALS 8.2.1
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 1.43 18.7 98.6 0.063 13.3 3.9 8980
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 1.43 1.47 91.9 0.68 2 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4MSB 1.43 18.7 8504 476 98.5 0.16984 0.16781 0.1729 0.20585 0.2082 RANDOM 19.014
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] 0.06 1.8 -1.79 1.28
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.31 r_sphericity_bonded 16.305 r_long_range_B_refined 5.106 r_long_range_B_other 5.051 r_scangle_other 3.919 r_rigid_bond_restr 3.866 r_scbond_it 3.405 r_scbond_other 3.404 r_angle_other_deg 3.183 r_angle_refined_deg 1.379
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.31 r_sphericity_bonded 16.305 r_long_range_B_refined 5.106 r_long_range_B_other 5.051 r_scangle_other 3.919 r_rigid_bond_restr 3.866 r_scbond_it 3.405 r_scbond_other 3.404 r_angle_other_deg 3.183 r_angle_refined_deg 1.379 r_chiral_restr 0.094 r_gen_planes_refined 0.021 r_bond_refined_d 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.003 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 424 Solvent Atoms 66 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing