☰ Navigation Tabs
16mer self-complementary duplex RNA with dA:s(2)U pair sequence 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MDX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, 30% v/v Polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 1.99 38.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.167 α = 90 b = 41.167 β = 90 c = 124.563 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 99 PIXEL DECTRIS PILATUS3 2M 2024-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.479 50 100 0.061 0.065 0.022 1 33 9.4 7122
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.479 1.51 100 0.573 0.609 0.204 0.901 3.5 8.6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.479 41.521 7109 348 99.789 0.172 0.1697 0.2115 0.2268 11.489
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 r_lrange_it 5.934 r_lrange_other 5.42 r_angle_other_deg 2.699 r_chiral_restr_other 2.401 r_angle_refined_deg 1.982 r_scangle_it 1.871 r_scangle_other 1.869 r_scbond_it 1.28 r_scbond_other 1.278 r_nbtor_refined 0.249
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.934 r_lrange_other 5.42 r_angle_other_deg 2.699 r_chiral_restr_other 2.401 r_angle_refined_deg 1.982 r_scangle_it 1.871 r_scangle_other 1.869 r_scbond_it 1.28 r_scbond_other 1.278 r_nbtor_refined 0.249 r_xyhbond_nbd_refined 0.233 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.171 r_nbd_other 0.143 r_nbd_refined 0.113 r_dihedral_angle_other_2_deg 0.083 r_symmetry_nbtor_other 0.08 r_symmetry_nbd_refined 0.08 r_chiral_restr 0.078 r_bond_other_d 0.029 r_metal_ion_refined 0.029 r_gen_planes_refined 0.027 r_bond_refined_d 0.011 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 335 Solvent Atoms 101 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing