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DNA Octaplex Formation with an I-Motif of A-Quartets: The Revised Crystal Structure of d(GCGAAAGC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UE3 1UE3(PDB code)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 sodium chloride, magnesium chloride, spermine 4HCl, 2-methyl-2,4-pentanediol, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.12 41.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.909 α = 90 b = 36.909 β = 90 c = 64.337 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2001-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.0 Photon Factory BL-18B
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 1.58 60 99.9 0.063 15.3 10.7 3359 11.5
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 1.58 1.64 99.4 0.305 3.3 6.2
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1UE3(PDB code) 1.6 8 3 3359 2764 270 88 0.19 0.19 0.211 RANDOM 32.3
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] 3.65 3.65 -7.3
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_angle_deg 2.1 c_improper_angle_d 1.47 c_bond_d 0.013 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_angle_deg 2.1 c_improper_angle_d 1.47 c_bond_d 0.013 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_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 164 Solvent Atoms 72 Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing