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RNA duplex containing UGGAA/UGGAA motif interacting with NCD molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9I9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.08 M Potassium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 6.0, 45% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.457 α = 90 b = 25.31 β = 102.485 c = 45.409 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 PIXEL DECTRIS PILATUS 6M 2018-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.55 46.113 98.4 0.999 16.17 6.03 3544
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.7 0.844
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 2.55 46.112 3543 185 98.471 0.2 0.1974 0.1999 0.2406 0.2367 65.778
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] -5.812 0.588 2.458 2.818
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 10.459 r_lrange_it 10.459 r_lrange_other 10.458 r_scangle_it 8.724 r_scangle_other 8.72 r_scbond_it 6.733 r_scbond_other 6.729 r_angle_other_deg 2.913 r_angle_refined_deg 1.938 r_symmetry_nbd_other 0.299
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 10.459 r_lrange_it 10.459 r_lrange_other 10.458 r_scangle_it 8.724 r_scangle_other 8.72 r_scbond_it 6.733 r_scbond_other 6.729 r_angle_other_deg 2.913 r_angle_refined_deg 1.938 r_symmetry_nbd_other 0.299 r_nbtor_refined 0.266 r_nbd_other 0.247 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.19 r_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_other 0.103 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.081 r_gen_planes_refined 0.012 r_gen_planes_other 0.012 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 642 Solvent Atoms 6 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing