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DNA duplex forming base triplets in minor groove
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BSE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 278 A solution containing 20mM Na-cacodylate, 10 mM MgCl2, 0.6mM DNA was mixed in a 1:1 ratio with a solution containing 56.25% v/v (+/-)-2-methyl-2,4-pentanediol, 30 mM Na-cacodylate pH 6.0, 30 mM Na-cacodylate 3H2O, 12mM SrCl2 6H2O. Total drop volume was 400nL
Crystal Properties Matthews coefficient Solvent content 2.74 55.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.833 α = 90 b = 39.833 β = 90 c = 58.964 γ = 90
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 RIGAKU HyPix-6000HE 2022-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 19.65 99.9 0.15 0.071 0.99 9.4 10.7 6283 26.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 1.1 0.79
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 2 18.87 1.34 6244 326 99.71 0.1929 0.1907 0.1906 0.2353 0.2342 33.22
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 33.0283 f_angle_d 0.6321 f_chiral_restr 0.0395 f_bond_d 0.0041 f_plane_restr 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 550 Solvent Atoms 92 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction Aimless data scaling SHELXDE phasing