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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, SITTING DROP 7 293 0.04m sodium cacodylate buffer, 0.08M NaCCl, 0.12m KCl, 0.02m MgCl2, 0.012m spermine tetra hydrochloride, 35% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.175 α = 90 b = 40.59 β = 90 c = 65.399 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 1.000670 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 1.99 50 96.5 0.038 0.022 21.23 3.55 4775 4315 2 4
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 1.99 2.11 94.6 0.217 5.81 3.27
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 1.99 50 4775 4315 334 96.5 0.2548 0.2518 0.2518 0.236 0.3281 0.3022 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 1 515.5
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.075 s_angle_d 0.073 s_bond_d 0.007 s_non_zero_chiral_vol 0.006 s_anti_bump_dis_restr 0.005 s_from_restr_planes 0.0005 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 29 Heterogen Atoms 2
Software Software Software Name Purpose RemDAq data collection PHASER phasing SHELXL-97 refinement XDS data reduction XDS data scaling