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Complicated water orientations in the minor groove of B-DNA decamer D(CCATTAATGG)2 observed by neutron diffraction measurements
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WQY PDB ENTRY 1WQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH (D2O) 7 279 30% MPD, 0.1M MAGNESIUM CHLORIDE, 0.1M SODIUM CACODYLATE, 0.002M DNA, pD 6.6, pH 7.0, BATCH (D2O), temperature 279K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.9 α = 90 b = 32.9 β = 90 c = 96.1 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 279 IMAGE PLATE JAERI BIX-4 2003-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR JRR-3M BEAMLINE 1G-A 2.60 JRR-3M 1G-A
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 3 100 63.1 0.233 5.803 1.23 1420 896 25.5
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 3 3.18 62.4 0.245 3.633 1.2 213
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 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WQY 3 30 1 1386 879 79 63.4 0.252 0.252 0.274 RANDOM 7
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]
RMS Deviations Key Refinement Restraint Deviation c_improper_angle_d 1.16 c_angle_deg 1.06 c_bond_d 0.026 c_dihedral_angle_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing