☰ Navigation Tabs
Racemic compound of RNA duplexes.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 0.2 M zinc acetate, 0.1 M cacodylate buffer, 18% w/v polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 1.96 37.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21 α = 105.088 b = 25.93 β = 96.628 c = 38.53 γ = 91.952
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 PILATUS 6M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.283 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 37 89.4 0.079 0.998 6.88 3.54 11141
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 86.3 0.967 0.797 0.89 3.51
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2GQ6 1.5 36.892 11127 581 89.388 0.195 0.1917 0.1997 0.2535 0.2624 20.501
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] -0.906 0.482 -0.118 2.021 -0.228 -0.839
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.185 r_lrange_other 3.593 r_scangle_it 1.853 r_scangle_other 1.852 r_angle_refined_deg 1.526 r_scbond_it 1.344 r_scbond_other 1.343 r_angle_other_deg 1.193 r_symmetry_nbd_other 0.277 r_nbtor_refined 0.25
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.185 r_lrange_other 3.593 r_scangle_it 1.853 r_scangle_other 1.852 r_angle_refined_deg 1.526 r_scbond_it 1.344 r_scbond_other 1.343 r_angle_other_deg 1.193 r_symmetry_nbd_other 0.277 r_nbtor_refined 0.25 r_symmetry_xyhbond_nbd_refined 0.24 r_xyhbond_nbd_refined 0.223 r_nbd_refined 0.221 r_metal_ion_refined 0.189 r_symmetry_nbd_refined 0.184 r_nbd_other 0.184 r_chiral_restr 0.061 r_symmetry_nbtor_other 0.061 r_symmetry_xyhbond_nbd_other 0.04 r_gen_planes_refined 0.02 r_bond_refined_d 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 676 Solvent Atoms 152 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing