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Dickerson dodecamer RNA duplex containing 2-F-6-aminopurine/U base pairing
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 drops containing 300nl 1 mM RNA and 300nl 10% 2-methyl-2,4-pentanediol (MPD), 40 mM sodium cacodylate, pH 7.0, 12 mM spermine 4HCl, 80 mM potassium chloride, 20 mM magnesium chloride and reservoir containing 40% MPD
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.105 α = 90 b = 34.983 β = 129.393 c = 32.127 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 Bruker PHOTON III 2022-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.3412
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 1.3 17.49 99.43 0.999 6.45 5.1 21611 13.43
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 1.3 1.38 0.187
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.3 17.49 0.03 16947 831 99.43 0.1769 0.1762 0.1895 0.1903 0.2004 17.58
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 21.4679 f_angle_d 1.661 f_chiral_restr 0.057 f_plane_restr 0.0262 f_bond_d 0.0142
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 257 Solvent Atoms 67 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing