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Structure of the poly-UG quadruplex (GUGUGU)4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 Diffraction quality crystals were eventually obtained by sitting drop vapor diffusion by mixing 2 uL of RNA with 2 uL of crystallization reagent containing 200 mM NaCl, 100 mM bis-tris pH 6.5 and 50 % PEG 550 MME. Crystals were vitrified by direct immersion into liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.04 39.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.821 α = 90 b = 32.821 β = 90 c = 57.97 γ = 90
Symmetry Space Group P 4 21 2
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 2018-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97619 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 1.052 21.726 95.9 0.077 0.0803 0.0221 0.995 18.35 12.98 14743
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) 1.052 1.071 62.9 0.8026 0.8838 0.3542 0.69 1.77 5.68 459
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SIRAS FREE R-VALUE 1.052 21.726 1.35 14726 1471 95.75 0.1496 0.1483 0.1484 0.1606 0.1606 13.57
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.3081 f_angle_d 1.0642 f_chiral_restr 0.0495 f_plane_restr 0.0194 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 252 Solvent Atoms 39 Heterogen Atoms 9
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling TRUNCATE data processing PHENIX refinement HKL2Map phasing