☰ Navigation Tabs
16mer self-complementary duplex RNA with s(2)C:I 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 6.5 293 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.2 43.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.405 α = 90 b = 43.405 β = 90 c = 123.136 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 EIGER2 S 9M 2024-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000050 ALS 8.2.1
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 1.54 41.05 99.9 0.052 0.058 0.025 0.998 19 9.4 6923 27.64
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 1.54 1.57 100 0.725 0.805 0.346 0.952 2.5 9.9
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 FREE R-VALUE 1.54 35.952 6881 687 99.279 0.225 0.2221 0.2253 0.2448 0.2457 29.087
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] -0.005 -0.002 -0.005 0.015
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.452 r_lrange_other 5.341 r_scangle_it 4.23 r_scangle_other 4.227 r_scbond_it 3.157 r_scbond_other 3.153 r_angle_refined_deg 2.481 r_angle_other_deg 0.832 r_xyhbond_nbd_refined 0.269 r_dihedral_angle_other_2_deg 0.24
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.452 r_lrange_other 5.341 r_scangle_it 4.23 r_scangle_other 4.227 r_scbond_it 3.157 r_scbond_other 3.153 r_angle_refined_deg 2.481 r_angle_other_deg 0.832 r_xyhbond_nbd_refined 0.269 r_dihedral_angle_other_2_deg 0.24 r_nbtor_refined 0.24 r_symmetry_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.211 r_nbd_other 0.15 r_chiral_restr 0.105 r_symmetry_nbd_refined 0.099 r_nbd_refined 0.092 r_symmetry_nbtor_other 0.086 r_gen_planes_refined 0.018 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 335 Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing