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Crystal structure of a DNA containing the rigid nitroxide spin-labeled nucleotide C-spin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KGK PDB ENTRY 1KGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 1.2 mM DNA in 10% 2-methane-2,4-pentanediol (MPD), 40 mM sodium cacodylate pH 6.0, 12 mM spermine-HCl, 80 mM NaCl, 12 mM KCl, 12 mM MgCl2 against a reserviore of 35% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.94 36.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.71 α = 90 b = 44.55 β = 90 c = 45.94 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944+ VariMax 2010-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 50 94.3 0.022 53.95 8.4 5955 5613
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 82.9 0.07 20.03 6.4 427
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 PDB ENTRY 1KGK 1.7004 16.824 1.37 5586 533 93.99 0.1632 0.1594 0.1556 0.1975 0.1914
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] -0.0439 -0.3863 0.4302
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 25.722 f_angle_d 1.738 f_chiral_restr 0.067 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 436 Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling