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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 7 293 0.04M sodium cacodylate buffer, 0.08M sodium chloride, 0.012M spermine tetra hydrochloride, 30% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.98 46.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.513 α = 90 b = 41.602 β = 90 c = 66.044 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 2012-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 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 1.831 41.6 97.5 0.034 0.021 24.06 3.68 6201
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 1.831 1.94 96.6 0.216 6.65 3.62
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 1.831 35.2 6201 6119 435 97.5 0.251 0.233 0.233 0.2213 0.306 0.2874 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 528.6
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.07 s_angle_d 0.028 s_from_restr_planes 0.012 s_anti_bump_dis_restr 0.008 s_bond_d 0.007 s_non_zero_chiral_vol 0.006 s_similar_dist s_zero_chiral_vol s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 490 Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose RemDAq data collection PHASER phasing SHELXL-97 refinement XDS data reduction XDS data scaling