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Dickerson dodecamer RNA duplex containing a modified base with a 2-F-6-aminopurine/G mismatch.
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 2.33 44.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.156 α = 90 b = 35.022 β = 128.091 c = 31.212 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 2022-07-14 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 1.12 15.8 98.59 0.998 12.46 8.7 13040 10.42
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 1.12 1.16 0.603
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.12 15.8 13001 1282 97.89 0.1653 0.1642 0.1721 0.1855 0.1888 16.1
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 20.896 f_angle_d 1.5093 f_chiral_restr 0.0514 f_plane_restr 0.0244 f_bond_d 0.0116
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 167 Solvent Atoms 91 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement SAINT data reduction PROTEUM PLUS data scaling MOLREP phasing