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Crystal structure analysis of the DNA quadruplex d(TGGGGT) S1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 244D NDB ENTRY UDF036
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 MPD, sodium cacodylate, magnesium chloride, spermine tetrahydrochlorhide, thallium acetate, lysine-anthraquinone, d(TGGGGT), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.01 38.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.259 α = 83.73 b = 35.41 β = 61.78 c = 32.057 γ = 76.68
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9800, 0.9772, 0.9076 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 20 0.06 3.16 5055 12.8
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) 2.2 2.28 83.3 0.11 455
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT NDB ENTRY UDF036 2.2 18.5 2 5055 4721 503 87.9 0.195 0.173 0.173 0.193 0.239 RANDOM 10.8
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] -0.42 0.52 -1.96 -4.5 4.91
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_scangle_it 1.95 c_scbond_it 1.49 c_improper_angle_d 1.01 c_angle_deg 0.7 c_mcbond_it 0.02 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_scangle_it 1.95 c_scbond_it 1.49 c_improper_angle_d 1.01 c_angle_deg 0.7 c_mcbond_it 0.02 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 966 Solvent Atoms 112 Heterogen Atoms 8
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing