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DNA DECAMER WITH AN ENGINEERED CROSSLINK IN THE MINOR GROOVE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BD1 BDJ017
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 MPD, CALCIUM CHLORIDE, SODIUM CHLORIDE, SPERMINE TETRACHLORIDE, SODIUM CACODYLATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.13 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.435 α = 90 b = 43.18 β = 90 c = 72.412 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 IMAGE PLATE MARRESEARCH 1998-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C NSLS X26C
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 1.55 13 95.5 0.078 9 4 62990 62990 14.7
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 1.55 1.61 98 0.32 3 4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT BDJ017 1.55 13 15525 15525 782 95.7 0.2031 0.2031 0.203 0.232 RANDOM 18.3
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] 3.895 -2.358 -1.537
RMS Deviations Key Refinement Restraint Deviation c_mcangle_it 4.824 c_mcbond_it 3.938 c_scangle_it 3.828 c_scbond_it 2.875 c_angle_deg 1.53 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_mcangle_it 4.824 c_mcbond_it 3.938 c_scangle_it 3.828 c_scbond_it 2.875 c_angle_deg 1.53 c_bond_d 0.009 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 c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 820 Solvent Atoms 271 Heterogen Atoms 1
Software Software Software Name Purpose AMoRE phasing CNS refinement MAR345 data collection SCALEPACK data scaling