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5-Methylcytosine modified DNA oligomer
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 6 298 0.04M sodium cacodylate buffer, 0.08M NaCl, 0.02M MgCl2, 0.012M spermine tetra hydrochloride, 35% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.29 46.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.495 α = 90 b = 40.4 β = 90 c = 65.5 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) 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 1.412 40.4 92.8 30.59 3.61 24635 22852 4 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.412 1.5 97.1 8.12 3.72 3958
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1.412 40.4 2 4 24635 22852 1235 92.8 0.178 0.177 0.177 0.1696 0.215 0.1955 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 611
RMS Deviations Key Refinement Restraint Deviation s_from_restr_planes 0.0636 s_angle_d 0.0388 s_similar_adp_cmpnt 0.0262 s_bond_d 0.0183 s_non_zero_chiral_vol 0.0156 s_anti_bump_dis_restr 0.0141 s_rigid_bond_adp_cmpnt 0.012 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 488 Solvent Atoms 127 Heterogen Atoms 1
Software Software Software Name Purpose RemDAq data collection PHASER phasing SHELXL-97 refinement XDS data reduction XDS data scaling