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Crystal structure of a double-ENE RNA stability element in complex with a 28-mer poly(A) RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other dENE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 50 mM sodium cacodylate, pH 7.0, 9 mM MgCl2, 1.8 mM cobalt (III) hexamine chloride, 0.9 mM spermidine, 2.5 mM spermine and 5% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.51 64.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.973 α = 90 b = 93.973 β = 90 c = 202.171 γ = 120
Symmetry Space Group P 64 2 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 PILATUS3 6M 2019-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9272 APS 24-ID-C
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 2.89 50 95.1 0.147 0.151 0.037 0.994 17.05 16.4 11859
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 2.89 3 3.293 3.45 0.979 0.199 0.66 10.2
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 dENE 2.89 47.03 11269 581 95.1 0.1862 0.1842 0.1832 0.2254 0.2316 RANDOM 108.846
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] 0.7 0.35 0.7 -2.28
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.951 r_angle_other_deg 1.675 r_chiral_restr 0.138 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2324 Solvent Atoms Heterogen Atoms 121
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction