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Crystal structure of RNAs A treated with sodium cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 292 0.1M sodium acetate buffer pH 5.5. reservoir solution containing 24-34% (NH4)2SO4, 0.1M sodium acetate buffer pH 5.5, and super-saturated solution of NaCl.
Crystal Properties Matthews coefficient Solvent content 2.79 55.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.329 α = 90 b = 64.329 β = 90 c = 64.102 γ = 120
Symmetry Space Group P 32 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 CMOS BRUKER PHOTON 100 2023-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5406
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 2.22 22.71 99.3 0.96 1.44 10.5 7822 16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.22 0.521
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1EIC 2.22 22.71 7462 342 99.38 0.2034 0.20091 0.2073 0.25752 0.2606 RANDOM 15.002
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.531 r_dihedral_angle_4_deg 18.857 r_dihedral_angle_3_deg 15.706 r_dihedral_angle_1_deg 7.799 r_long_range_B_refined 4.741 r_long_range_B_other 4.436 r_scangle_other 2.245 r_mcangle_it 2.197 r_mcangle_other 2.195 r_angle_refined_deg 1.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.531 r_dihedral_angle_4_deg 18.857 r_dihedral_angle_3_deg 15.706 r_dihedral_angle_1_deg 7.799 r_long_range_B_refined 4.741 r_long_range_B_other 4.436 r_scangle_other 2.245 r_mcangle_it 2.197 r_mcangle_other 2.195 r_angle_refined_deg 1.517 r_scbond_it 1.328 r_angle_other_deg 1.317 r_scbond_other 1.295 r_mcbond_other 1.254 r_mcbond_it 1.252 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 951 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Aimless data scaling MOLREP phasing