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Dickerson dodecamer RNA duplex containing an A/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 grown in drops containing 0.3 microliter of 1.0 mM RNA and 0.3 microliter of 10% 2-methyl-2,4-pentanediol (MPD), 12 mM spermine-4HCl, 20 mM MgCl2, 80 mM KCl, 40 mM sodium cacodylate, pH 7.0. The reservoirs contained 70 microliters 40% 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.168 α = 90 b = 34.964 β = 128.929 c = 31.91 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 2022-08-18 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 1.03 16.01 98.9 0.996 4.41 4.5 37549 10.01
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 1.03 1.06 0.07
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 1.03 16.01 0.01 33859 1714 98.86 0.1724 0.1718 0.1605 0.1831 0.1768 15.39
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 20.4506 f_angle_d 1.4355 f_chiral_restr 0.064 f_plane_restr 0.0298 f_bond_d 0.0098
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 255 Solvent Atoms 82 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing