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Crystal structure of r(GU)11G-NMM complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 The RNA smaple was prepared by mixing 1.44mM (GU)11G RNA and 1.44 mM NMM in 10 mM Tris, pH 7.03, and 100 mM KCl. An equal volume of RNA sample solution and reservoir solution were mixed and suspended over the reservoir solution consisting of 0.5 M Na/K tartarate, 0.1 M TrisHCl, pH 8.5, 5 mM NaOH. Cryoprotection: reservoir solution supplemented with 30% ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.475 α = 90 b = 42.483 β = 90.09 c = 21.607 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 9M 2020-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1271 APS 21-ID-D
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 1.97 21.61 99.02 0.05163 0.05684 0.0231 0.998 16.09 6.7 5407 63.54
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 1.97 2.04 99.25 0.7553 0.8172 0.3083 0.966 1.57 6.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.97 21.61 4922 476 97.35 0.27053 0.26869 0.3193 0.29145 0.3388 RANDOM 63.361
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] 20.86 9.54 9.07 -29.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 10.721 r_long_range_B_refined 6.788 r_long_range_B_other 6.784 r_scangle_other 4.182 r_scbond_it 2.952 r_scbond_other 2.949 r_angle_other_deg 1.096 r_angle_refined_deg 1.072 r_chiral_restr 0.056 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 10.721 r_long_range_B_refined 6.788 r_long_range_B_other 6.784 r_scangle_other 4.182 r_scbond_it 2.952 r_scbond_other 2.949 r_angle_other_deg 1.096 r_angle_refined_deg 1.072 r_chiral_restr 0.056 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_dihedral_angle_1_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 493 Solvent Atoms Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AutoSol phasing