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DNA dodecamer containing 5-hydroxymethyl cytosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPN PDB ENTRY 1DPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.04M sodium cacodylate buffer, 0.08M potassium chloride, 0.012M sodium chloride, 0.012M spermine tetra hydrochloride, 37% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.637 α = 90 b = 41.767 β = 90 c = 63.997 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 PIXEL DECTRIS PILATUS 2M-F 2012-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00067 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.662 41.78 99.4 0.025 0.0152 28.66 3.61 8542 7781 4 2
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 1.662 1.76 99 0.202 6.93 3.71
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1DPN 1.662 41.78 8542 7781 427 99.7 0.237 0.237 0.2193 0.276 0.2383 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 552.3
RMS Deviations Key Refinement Restraint Deviation s_angle_d 0.0293 s_similar_adp_cmpnt 0.0267 s_from_restr_planes 0.0149 s_bond_d 0.0087 s_rigid_bond_adp_cmpnt 0.0084 s_non_zero_chiral_vol 0.0082 s_anti_bump_dis_restr 0.008 s_similar_dist s_zero_chiral_vol s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 490 Solvent Atoms 68 Heterogen Atoms 2
Software Software Software Name Purpose RemDAq data collection PHASER phasing SHELXL-97 refinement XDS data reduction XDS data scaling