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Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2 at 1.7 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1mM DNA, 50mM sodium cacodylate buffer, 8mM Zncl2, 10mM spermine, 40% MPD
Crystal Properties Matthews coefficient Solvent content 2.03 59.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.283 α = 90 b = 29.283 β = 90 c = 88.213 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 CCD MARMOSAIC 225 mm CCD Bent collimating mirror 2013-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.282 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.69 27.792 98.4 0.045 0.049 0.999 21.74 16064 -3 27.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.8 92.9 0.276 0.298 0.968 5.69
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3V9D 1.694 27.792 1.45 16056 1591 98.32 0.1914 0.1884 0.1891 0.2195 0.2204 Random 34.449
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 14.044 f_angle_d 1.553 f_chiral_restr 0.078 f_bond_d 0.013 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 568 Solvent Atoms 46 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction PHASER phasing PDB_EXTRACT data extraction