☰ Navigation Tabs
16mer self-complementary duplex RNA with D:C pair sequence 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ND4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 10 mM Magnesium chloride hexahydrate, 50 mM HEPES sodium pH 7.0, 4.0 M Lithium chloride
Crystal Properties Matthews coefficient Solvent content 2.22 44.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.501 α = 90 b = 42.501 β = 90 c = 129.967 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 6M 2023-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 2.0.1 1.033216 ALS 2.0.1
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 1.42 50 96.2 0.065 0.069 0.024 0.983 30 7.1 8586
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 1.42 1.44 64.5 0.268 0.345 0.214 0.9 2.8 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.42 35.414 8160 379 91.398 0.216 0.2146 0.222 0.2376 0.2466 11.558
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] -0.001 -0.001 -0.001 0.004
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.259 r_lrange_other 5.02 r_angle_refined_deg 2.37 r_scangle_it 2.319 r_scangle_other 2.317 r_scbond_it 1.598 r_scbond_other 1.596 r_angle_other_deg 0.637 r_dihedral_angle_other_2_deg 0.575 r_nbd_refined 0.426
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.259 r_lrange_other 5.02 r_angle_refined_deg 2.37 r_scangle_it 2.319 r_scangle_other 2.317 r_scbond_it 1.598 r_scbond_other 1.596 r_angle_other_deg 0.637 r_dihedral_angle_other_2_deg 0.575 r_nbd_refined 0.426 r_xyhbond_nbd_refined 0.301 r_nbtor_refined 0.251 r_symmetry_nbd_other 0.206 r_nbd_other 0.117 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.086 r_symmetry_nbd_refined 0.081 r_symmetry_xyhbond_nbd_refined 0.064 r_gen_planes_refined 0.029 r_bond_refined_d 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 337 Solvent Atoms 79 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing